├── LICENSE ├── README.md ├── add_caller.pl ├── add_dnp.pl ├── add_rc.pl ├── cocoon.pl ├── combine_variant.pl ├── dbsnp_filter.pl ├── extract_somatic_other.pl ├── filter_large_indel.pl ├── filter_mutect.pl ├── filter_mutect1.7.pl ├── filter_mutect1.8.pl ├── generate_coding_report.pl ├── generate_final_report.pl ├── generate_maf.pl ├── genomevip_label.pl ├── get_strelka_passed_snv_indel.pl ├── merge_mutect.pl ├── pindel_filter.v0.5.pl ├── qc_vcf.pl ├── remove_largeindel.pl ├── remove_nearby_snv.pl ├── set_envvars ├── snv_filter.pl ├── somaticwrapper.pl ├── splice_site_check.pl ├── strelka.ini ├── strelka.ini.wgs ├── vaf_all_callers.pl ├── vaf_filter.pl ├── vaf_filter_hg19.pl ├── vaf_filter_hg19_v1.1.pl ├── vaf_filter_michigan_washu.pl ├── vaf_filter_v1.1.pl ├── vaf_filter_v1.2.pl ├── vaf_filter_v1.3.pl ├── vaf_filter_v1.4.pl ├── vcf2maf.pl ├── vep_annotator.pl ├── work_log_run_alchemist_b1 ├── work_log_run_alchemist_b10 ├── work_log_run_alchemist_b11 ├── work_log_run_alchemist_b12 ├── work_log_run_alchemist_b2 ├── work_log_run_alchemist_b4 ├── work_log_run_alchemist_b6 ├── work_log_run_alchemist_b8 ├── work_log_run_alchemist_b9 ├── work_log_run_alchemist_unfinished ├── work_log_run_alchemist_unfinished2 ├── work_log_run_alchemist_unfinished3 ├── work_log_run_confirmatory_gbm_b1 ├── work_log_run_confirmatory_gbm_realign.b1 ├── work_log_run_confirmatory_gbm_realign.b2 ├── work_log_run_ctspkirc ├── work_log_run_dlbcl ├── work_log_run_gbm ├── work_log_run_htan_brca ├── work_log_run_mild ├── work_log_run_mild_v102 ├── work_log_run_mild_wgs ├── work_log_run_pecgsb1 └── work_log_run_test /README.md: -------------------------------------------------------------------------------- 1 | 2 | # Somaticwrapper version 2.2, compute1 # 3 | 4 | Detect somatic variants from tumor and normal WGS/WXS data (HG38 reference). SomaticWrapper pipeline is a fully automated and modular software package designed for detection of somatic variants from tumor and normal exome data. It works on LSF job scheduler and can run multiple jobs in parallel. Multiple standard variant calling tools are included in the pipeline such as varscan2, strelka2, mutect1 and pindel. The final called variant can be found from dnp.annotated.maf for all variants and dnp.annotated.coding.maf for coding variants. 5 | 6 | SNV calls are intersecting results from 2 over 3 callers (Strelka2, Mutect1, and VarScan2). 7 | 8 | Indel calls are called by 2 over 3 callers (Strelka2, Varscan2 and pindel). 9 | 10 | Improvements compared to version v2.1: 11 | 12 | 1. Remove indels > 100 nt before annotation 13 | 14 | 2. Fix false alarm for step 7 15 | 16 | ## Usage ## 17 | 18 | Step 0: set environment for LSF job on compute1 by adding the following to ~/.bashrc file: 19 | 20 | export PATH=/storage1/fs1/songcao/Active/Software/anaconda3/bin:$PATH 21 | 22 | export STORAGE1=/storage1/fs1/songcao/Active 23 | 24 | export STORAGE2=/storage1/fs1/dinglab/Active 25 | 26 | export STORAGE3=/storage1/fs1/m.wyczalkowski/Active 27 | 28 | export LSF_DOCKER_VOLUMES="$STORAGE1:$STORAGE1 $STORAGE2:$STORAGE2 $STORAGE3:$STORAGE3" 29 | 30 | then run "source ~/.bashrc" 31 | 32 | 33 | Step1: Enter the directory where you downloaded somaticwrapper pipeline 34 | 35 | Step2: Type the coommand line: perl somaticwrapper.pl --srg --sre --wgs --rdir --ref --log --q --mincovt --mincovn --minvaf --maxindsize --exonic --smg --groupname --users --step 36 | 37 | rdir = full path of the folder holding files for this sequence run (user must provide) 38 | 39 | log = full path of the folder for saving log file; usually upper folder of rdir 40 | 41 | srg = bam having read group or not: 1, yes and 0, no (default 1) 42 | 43 | sre = re-run: 1, yes and 0, no (default 0) 44 | 45 | wgs = 1 if it is wgs data and otherwise it is 0; If you want to output the maf for all variants, set exonic to 0 46 | 47 | groupname = job group name: Format; users/groupname 48 | 49 | users = user name for job group: Format; users/groupname 50 | 51 | step run this pipeline step by step. (user must provide) 52 | 53 | ref: the human reference: 54 | 55 | q: which queue for submitting job; research-hpc, ding-lab, long (default) 56 | 57 | mincovt: minimum coverage for tumor: default >=14 58 | 59 | mincovn: minimum coverage for normal: default >=8 60 | 61 | minvaf: minimum somatic vaf: default >=0.05 62 | 63 | maxindsize: default <= 100 64 | 65 | exonic: output exonic region: 1 Yes, 0 No, Default Yes 66 | 67 | smg: smg gene list that escapes the 0.05 vaf cut-off 68 | 69 | 70 | 71 | [1] Run streka 72 | 73 | [2] Run Varscan 74 | 75 | [3] Run Pindel 76 | 77 | [4] Run mutect 78 | 79 | [5] Parse mutect result 80 | 81 | [6] Parse streka result 82 | 83 | [7] Parse VarScan result 84 | 85 | [8] Parse Pindel 86 | 87 | [9] QC vcf files 88 | 89 | [10] Merge vcf files 90 | 91 | [11] Generate maf file 92 | 93 | [12] Generate merged maf file 94 | 95 | [13] DNP annotation 96 | 97 | [14] Clean unnecessary intermediate files 98 | 99 | ## Contact ## 100 | 101 | Song Cao, scao@wustl.edu 102 | -------------------------------------------------------------------------------- /add_caller.pl: -------------------------------------------------------------------------------- 1 | ### add read counts and vafs for ref and var to maf file ## 2 | ### Song Cao ## 3 | 4 | #!/usr/bin/perl 5 | use strict; 6 | use warnings; 7 | (my $usage = <$f_out"); 27 | 28 | foreach my $l (`cat $f_maf`) 29 | { 30 | 31 | my $ltr=$l; 32 | chomp($ltr); 33 | my @temp=split("\t",$ltr); 34 | my $i; 35 | if($ltr=~/^Hugo/) { for($i=0;$i<=44;$i++) { print OUT $temp[$i],"\t"; } print OUT "callers"; for($i=45;$i) 62 | { 63 | my $l2=$_; 64 | chomp($l2); 65 | #print $l2,"\n"; 66 | 67 | if($l2=~/^#/) { next; } 68 | #my $temp7=$temp[7]; 69 | 70 | my @temp2=split("\t",$l2); 71 | my $info2=$temp2[7]; 72 | 73 | my $ref=$temp2[3]; 74 | my $var=$temp2[4]; 75 | my $equal=0; 76 | #print $ref,"\t",$var,"\n"; 77 | for(my $i=0;$i; 93 | my @temp3=split(";",$info2); 94 | my $info3=$temp3[-1]; 95 | $info3=~s/set=//g; 96 | print $id, "\t",$info3,"\n"; 97 | $caller{$id}=$info3; 98 | } 99 | 100 | close IN; 101 | } 102 | 103 | # add read counts for tumor and normal ## 104 | ## t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count 105 | ## 40-44 106 | my $pos2=$temp[5]; 107 | 108 | # if($temp[12] eq "-") 109 | # { 110 | # $pos-=1; 111 | # } 112 | 113 | my $id2=$temp[4]."_".$pos2; 114 | print $id2,"\n"; 115 | #; 116 | 117 | if(defined $caller{$id2}) 118 | { 119 | 120 | my $callerinf=$caller{$id2}; 121 | print $callerinf,"\n"; 122 | #; 123 | #print $id2,"\n"; 124 | # print $vaf,"\n"; 125 | # print $sn_1,"\n"; 126 | #; 127 | #my @temp3=split("_",$vaf); 128 | #my $t_depth=$temp3[2]+$temp3[3]; 129 | #my $t_ref_count=$temp3[2]; 130 | #my $t_alt_count=$temp3[3]; 131 | 132 | #my $n_depth=$temp3[0]+$temp3[1]; 133 | #my $n_ref_count=$temp3[0]; 134 | #my $n_alt_count=$temp3[1]; 135 | 136 | print OUT $temp[0]; 137 | 138 | for(my $i=1;$i<=44;$i++) 139 | { 140 | print OUT "\t",$temp[$i]; 141 | } 142 | 143 | print OUT "\t",$callerinf; 144 | 145 | for(my $i=45;$i$maf_out"); 24 | 25 | ### merged ### 26 | 27 | my $status_mnp=0; 28 | my $ref=""; 29 | my $var=""; 30 | my $prot1=""; 31 | my $prot2=""; 32 | my $effect=""; 33 | my $c=""; 34 | 35 | foreach my $l (`cat $maf_mnp`) 36 | { 37 | my $ltr=$l; 38 | chomp($ltr); 39 | my @l=split("\t",$ltr); 40 | 41 | if($ltr=~/^Hugo/) { next; } 42 | else 43 | { 44 | 45 | if($ltr=~/^#/) 46 | { 47 | if($ltr=~/Merged\=Yes/) 48 | { $status_mnp=1; } 49 | elsif($ltr=~/2\s+1\s+Merged=No\(different codons\)/) 50 | { 51 | $status_mnp=2; 52 | $ref=""; 53 | $var=""; 54 | $prot1=""; 55 | $prot2=""; 56 | $effect=""; 57 | $c=""; 58 | #print $ltr,"\n"; 59 | #; 60 | } 61 | elsif($ltr=~/2\s+1\s+Merged=No\(not cds\)/) 62 | { 63 | $status_mnp=2; 64 | $ref=""; 65 | $var=""; 66 | $prot1=""; 67 | $prot2=""; 68 | $effect=""; 69 | $c=""; 70 | #print $ltr,"\n"; 71 | #; 72 | }else { 73 | $status_mnp=0; 74 | } 75 | } 76 | else 77 | { 78 | if($status_mnp==1) 79 | { 80 | #my @l=split("\t",$ltr); 81 | my $sn=$l[15]; 82 | $mnp_infor{$sn}{$l[4]}{$l[5]}=$ltr; 83 | $mnp_end{$sn}{$l[4]}{$l[5]}=$l[6]; 84 | } 85 | 86 | if($status_mnp==2) 87 | { 88 | $ref.=$l[10]; 89 | $var.=$l[12]; 90 | 91 | if($prot2 eq "") 92 | { 93 | $c=$l[34]; 94 | $prot1=$l[35]; 95 | $prot2=$l[36]; 96 | } 97 | else 98 | { 99 | $c.=";".$l[34]; 100 | $prot1.=";".$l[35]; 101 | $prot2.=";".$l[36]; 102 | } 103 | 104 | #print $l[9],"\n"; 105 | 106 | if($l[8]=~/Splice_Site/) { $effect=$l[8]; } 107 | ## silent ## 108 | if($l[8]=~/Silent/ && !($effect=~/Nonsense_Mutation/ || $effect=~/Missense_Mutation/ || $effect=~/Splice_Site/ || $effect=~/Nonstop_Mutation/)) 109 | { 110 | $effect=$l[8]; 111 | } 112 | 113 | if($l[8]=~/Missense_Mutation/ && !($effect=~/Nonsense_Mutation/ || $effect=~/Splice_Site/ || $effect=~/Nonstop_Mutation/)) { 114 | $effect=$l[8]; 115 | } 116 | 117 | if($l[8]=~/Nonstop_Mutation/ && !($effect=~/Nonsense_Mutation/ || $effect=~/Splice_Site/)) { 118 | $effect=$l[8]; 119 | } 120 | 121 | if($l[8]=~/Nonsense_Mutation/ && !($effect=~/Splice_Site/)) { 122 | $effect=$l[8]; 123 | } 124 | 125 | if(length($ref)==2 && length($var)==2) 126 | { 127 | my $start=$l[5]-1; 128 | my $end=$l[5]; 129 | 130 | #print $ref,"\t",$var,"\t",$effect,"\t",$start,"\t",$c,"\t",$prot1,"\t",$prot2,"\n"; 131 | #; 132 | $mnp_infor{$l[15]}{$l[4]}{$start}=join("\t", @l[0..4])."\t$start\t$end\t$l[7]\t$effect\tMNP\t$ref\t$var\t$var\t".join("\t",@l[13..33])."\t".$c."\t".$prot1."\t".$prot2."\t".join("\t", @l[37..$#l]); 133 | $mnp_end{$l[15]}{$l[4]}{$start}=$end; 134 | } 135 | 136 | } 137 | 138 | } 139 | 140 | } 141 | } 142 | 143 | my $removed=0; 144 | my $chr; 145 | my $begin; 146 | my $end; 147 | 148 | foreach my $l (`cat $maf_in`) 149 | { 150 | 151 | my $ltr=$l; 152 | chomp($ltr); 153 | if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; } 154 | else 155 | { 156 | my @l=split("\t",$ltr); 157 | if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; } 158 | else { 159 | my @l=split("\t",$ltr); 160 | my $sn=$l[15]; 161 | 162 | ## mnp ## 163 | 164 | if(defined $mnp_infor{$sn}{$l[4]}{$l[5]}) 165 | { 166 | print OUT $mnp_infor{$sn}{$l[4]}{$l[5]},"\n"; 167 | #print $sn,"\t",$l[4],"\t",$l[5],"\n"; 168 | #print $mnp_infor{$sn}{$l[4]}{$l[5]},"\n"; 169 | #; 170 | $removed=1; 171 | $chr=$l[4]; 172 | $begin=$l[5]; 173 | $end=$mnp_end{$sn}{$l[4]}{$l[5]} 174 | } 175 | else 176 | { 177 | if($removed==1 && $l[4] eq $chr && ($l[5]>=$begin && $l[5]<=$end)) 178 | { 179 | #print $l[4],"\t",$l[5],"\n"; 180 | #; 181 | next; 182 | } 183 | else { print OUT $ltr,"\n"; $removed=0; } 184 | } 185 | 186 | } 187 | } 188 | 189 | } 190 | 191 | 192 | close IN; 193 | close MNP; 194 | close OUT; 195 | -------------------------------------------------------------------------------- /add_rc.pl: -------------------------------------------------------------------------------- 1 | ### add read counts and vafs for ref and var to maf file ## 2 | ### Song Cao ## 3 | 4 | #!/usr/bin/perl 5 | use strict; 6 | use warnings; 7 | (my $usage = <$f_out"); 19 | 20 | foreach my $l (`cat $f_maf`) 21 | { 22 | 23 | my $ltr=$l; 24 | chomp($ltr); 25 | my @temp=split("\t",$ltr); 26 | 27 | if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; } 28 | 29 | else { 30 | 31 | $sn_1=$temp[15]; $sn_1=~s/_T$//g; 32 | 33 | if($sn_2 eq "" || $sn_2 ne $sn_1) 34 | { 35 | 36 | %vaf_rc=(); 37 | $sn_2=$sn_1; 38 | 39 | my $f_vaf=$run_dir."/".$sn_1."/merged.withmutect.vaf"; 40 | open(IN,"<$f_vaf"); 41 | my $id; 42 | 43 | my $n_ref; 44 | my $n_var; 45 | my $t_ref; 46 | my $t_var; 47 | 48 | while() 49 | { 50 | my $l2=$_; 51 | chomp($l2); 52 | my @temp2=split("\t",$l2); 53 | my $ref=$temp2[3]; 54 | my $var=$temp2[4]; 55 | my $equal=0; 56 | #print $ref,"\t",$var,"\n"; 57 | for(my $i=0;$i; 78 | $vaf_rc{$id}=$n_ref."_".$n_var."_".$t_ref."_".$t_var; 79 | } 80 | 81 | close IN; 82 | } 83 | 84 | # add read counts for tumor and normal ## 85 | ## t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count 86 | ## 40-45 87 | my $pos2=$temp[5]; 88 | 89 | # if($temp[12] eq "-") 90 | # { 91 | # $pos-=1; 92 | # } 93 | 94 | my $id2=$temp[4]."_".$pos2; 95 | if(defined $vaf_rc{$id2}) 96 | { 97 | my $vaf=$vaf_rc{$id2}; 98 | 99 | #print $id2,"\n"; 100 | # print $vaf,"\n"; 101 | # print $sn_1,"\n"; 102 | #; 103 | my @temp3=split("_",$vaf); 104 | my $t_depth=$temp3[2]+$temp3[3]; 105 | my $t_ref_count=$temp3[2]; 106 | my $t_alt_count=$temp3[3]; 107 | 108 | my $n_depth=$temp3[0]+$temp3[1]; 109 | my $n_ref_count=$temp3[0]; 110 | my $n_alt_count=$temp3[1]; 111 | 112 | print OUT $temp[0]; 113 | 114 | for(my $i=1;$i<39;$i++) 115 | { 116 | print OUT "\t",$temp[$i]; 117 | } 118 | 119 | print OUT "\t",$t_depth,"\t",$t_ref_count,"\t",$t_alt_count,"\t",$n_depth,"\t",$n_ref_count,"\t",$n_alt_count; 120 | for(my $i=45;$i$f_out"); 18 | 19 | foreach my $dir_s (`ls $run_dir`) 20 | { 21 | my $dir_s_f=$run_dir."/".$dir_s; 22 | if(-d $dir_s_f) 23 | { 24 | 25 | my %mut_inf=(); 26 | my %snv_varscan_tag=(); 27 | my %indel_varscan_tag=(); 28 | my %snv_strelka_tag=(); 29 | my %indel_strelka_tag=(); 30 | 31 | my $f_varscan_snv=$dir_s_f."/varscan/varscan.out.som_snv.current_final.gvip.Somatic.VEP.vcf"; 32 | my $f_varscan_indel=$dir_s_f."/varscan/varscan.out.som_indel.current_final.gvip.Somatic.VEP.vcf"; 33 | my $f_strelka_snv=$dir_s_f."/strelka/strelka_out/results/strelka.somatic_snv.current_final.gvip.Somatic.VEP.vcf"; 34 | my $f_strelka_indel=$dir_s_f."/strelka/strelka_out/results/strelka.somatic_indel.current_final.gvip.Somatic.VEP.vcf"; 35 | foreach my $v (`cat $f_varscan_snv`) 36 | { 37 | my $vtr=$v; 38 | chomp($vtr); 39 | if($vtr=~/^#/) 40 | { 41 | next; 42 | } 43 | my @temp=split("\t",$vtr); 44 | my $mut=$temp[0]."_".$temp[1]."_".$temp[3]."_".$temp[4]; 45 | $mut_inf{$mut}=$vtr; 46 | 47 | } 48 | } 49 | } 50 | -------------------------------------------------------------------------------- /dbsnp_filter.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | #---------------------------------- 3 | # @name GenomeVIP dbSNP annotation and filtering script 4 | # @author R. Jay Mashl 5 | # 6 | # @version 0.3 (rjm): add mode switch 7 | # @version 0.2 (rjm): workaround for stat on AWS 8 | # @version 0.1 (rjm): based on approach from Venkata Yellapantula 9 | #-------------------------------------- 10 | use strict; 11 | use warnings; 12 | 13 | use Cwd; 14 | use Carp; 15 | use FileHandle; 16 | use IO::File; 17 | use Getopt::Long; 18 | use POSIX qw( WIFEXITED ); 19 | use File::Temp qw/ tempfile /; 20 | #use File::stat; 21 | 22 | 23 | sub checksize { 24 | my ($dest,$src) = @_; 25 | my $fs = `wc -l < $dest`; 26 | if ( $fs == 0){ system("grep ^# $src > $dest"); } 27 | return 1; 28 | } 29 | 30 | # get paras from config file 31 | my (%paras); 32 | map { chomp; if(!/^[#;]/ && /=/) { @_ = split /=/; $_[1] =~ s/ //g; my $v = $_[1]; print $v."\n"; $_[0] =~ s/ //g; $paras{ (split /\./, $_[0])[-1] } = $v } } (<>); 33 | # map { print; print "\t"; print $paras{$_}; print "\n" } keys %paras; 34 | 35 | # Use uncompressed db to avoid being bitten by java compression bug 36 | my $anno=$paras{'rawvcf'}."dbsnp_anno.vcf"; 37 | if ($paras{'rawvcf'} =~ /\.vcf$/) { 38 | ($anno = $paras{'rawvcf'}) =~ s/\.vcf$/\.dbsnp_anno\.vcf/; 39 | } 40 | 41 | 42 | my $cmd = "java $ENV{'JAVA_OPTS'} -jar $paras{'annotator'} annotate -id $paras{'db'} $paras{'rawvcf'} > $anno"; 43 | print "$cmd\n"; 44 | system($cmd); 45 | checksize($anno, $paras{'rawvcf'}); 46 | if( exists $paras{'mode'} && $paras{'mode'} eq "filter" ) { 47 | $cmd = "java $ENV{'JAVA_OPTS'} -jar $paras{'annotator'} filter -n \" (exists ID) & (ID =~ 'rs' ) \" -f $anno > $paras{'passfile'}"; 48 | system($cmd); 49 | checksize($paras{'passfile'}, $anno); 50 | $cmd = "java $ENV{'JAVA_OPTS'} -jar $paras{'annotator'} filter \" (exists ID) & (ID =~ 'rs' ) \" -f $anno > $paras{'dbsnpfile'}"; 51 | system($cmd); 52 | checksize($paras{'dbsnpfile'}, $anno); 53 | $cmd = "rm -f $anno"; 54 | system($cmd); 55 | } 56 | 1; 57 | 58 | -------------------------------------------------------------------------------- /extract_somatic_other.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | # --------------------- 3 | # @name GenomeVIP utility to extract 'other' calls from varscan 4 | # @author R. Jay Mashl 5 | # @version 6 | # 7 | # @syntax extract_somatic_other.pl < source.vcf > destination.vcf 8 | # --------------------- 9 | use strict; 10 | use warnings; 11 | 12 | 13 | while(<>) { 14 | my @a = split /\t/; 15 | print $_ if( /^#/ || ($a[7] =~ /^SS=[05]/ || $a[7] =~ /;SS=[05]$/ || $a[7] =~ /;SS=[05];/) ); 16 | } 17 | -------------------------------------------------------------------------------- /filter_large_indel.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | use strict; 3 | use warnings; 4 | 5 | ## filter large indel (>100) in pindel output ## 6 | ## remove END pos in pindel vcf output, which can cause gatk merging problems ## 7 | 8 | my ($f_indel_in,$f_indel_out,$indel_max_size)=@ARGV; 9 | 10 | #my $indel_max_size=100; 11 | 12 | open(IN,"<$f_indel_in"); 13 | open(OUT,">$f_indel_out"); 14 | 15 | while() 16 | { 17 | my $ltr=$_; 18 | chomp($ltr); 19 | if($ltr=~/^#/) { 20 | if($ltr=~/^#CHROM/) { 21 | my @temphead=split("\t",$ltr); 22 | print OUT $temphead[0]; 23 | 24 | for(my $i=1;$i<=8;$i++) 25 | { 26 | print OUT "\t",$temphead[$i]; 27 | } 28 | 29 | if($temphead[9]=~/\.T$/ && $temphead[10]=~/\.N$/) { print OUT "\t","TUMOR","\t","NORMAL","\n"; last; } 30 | if($temphead[9]=~/\.N$/ && $temphead[10]=~/\.T$/) { print OUT "\t","NORMAL","\t","TUMOR","\n"; } 31 | 32 | } 33 | else { print OUT $ltr,"\n"; } 34 | } 35 | else { 36 | my @temp=split("\t",$ltr); 37 | my $ref=$temp[3]; 38 | my $var=$temp[4]; 39 | my $info=$temp[7]; 40 | $info=~s/END=\d+;//g; 41 | if(length($ref)>$indel_max_size || length($var)>$indel_max_size) { next; } 42 | else 43 | { 44 | print OUT $temp[0]; 45 | for(my $i=1;$i<=6;$i++) 46 | { 47 | print OUT "\t",$temp[$i]; 48 | } 49 | print OUT "\t",$info; 50 | for(my $i=8;$i<=10; $i++) 51 | { 52 | print OUT "\t",$temp[$i]; 53 | } 54 | print OUT "\n"; 55 | } 56 | } 57 | } 58 | 59 | close OUT; 60 | close IN; 61 | #my $f_m=$run_dir."/mutect/mutect.raw.vcf"; 62 | #my $f_filter_out=$run_dir."/mutect/mutect.filtered.vcf"; 63 | 64 | ### minimum vaf for tumor 0.05, column 10 ### 65 | ## maximum vaf for normal 0.02, column 11 ### 66 | ## minimum coverage 20 ### 67 | 68 | ### get the bam path ## 69 | -------------------------------------------------------------------------------- /filter_mutect.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | ### add the filtering for indel length ## 5 | ### mutect filtering ### 6 | 7 | use strict; 8 | use warnings; 9 | die unless @ARGV == 2; 10 | my ($f_m,$f_filter_out)=@ARGV; 11 | 12 | #my $f_m=$run_dir."/mutect/mutect.raw.vcf"; 13 | #my $f_filter_out=$run_dir."/mutect/mutect.filtered.vcf"; 14 | 15 | my $min_vaf_somatic=0.05; 16 | my $max_vaf_germline=0.02; 17 | my $min_coverage=20; 18 | 19 | open(IN,"<$f_m"); 20 | open(OUT,">$f_filter_out"); 21 | 22 | while() 23 | { 24 | my $l=$_; 25 | chomp($l); 26 | if($l=~/^#/) { print OUT $l,"\n"; } 27 | else { 28 | my @temp=split("\t",$l); 29 | my $tumor=$temp[9]; 30 | my $normal=$temp[10]; 31 | my @tempt=split(":",$tumor); 32 | my @tempn=split(":",$normal); 33 | my @readt=split(",",$tempt[1]); 34 | my @readn=split(",",$tempn[1]); 35 | my $tot_n=$readn[0]+$readn[1]; 36 | my $tot_t=$readt[0]+$readt[1]; 37 | my $vaf_t=$tempt[2]; 38 | my $vaf_n=$tempn[2]; 39 | if($temp[6] eq "PASS" && $vaf_t>=$min_vaf_somatic && $vaf_n<=$max_vaf_germline && $tot_n>=$min_coverage && $tot_t>=$min_coverage) 40 | { 41 | print OUT $l,"\n"; 42 | } 43 | } 44 | 45 | } 46 | 47 | 48 | -------------------------------------------------------------------------------- /filter_mutect1.7.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=2% 4 | ### mutect1.7 filtering ### 5 | 6 | use strict; 7 | use warnings; 8 | die unless @ARGV == 6; 9 | ### samtools ## 10 | 11 | my ($samtools,$f_m,$f_filter_out,$mincov_t,$mincov_n,$minvaf)=@ARGV; 12 | 13 | #my $f_m=$run_dir."/mutect/mutect.raw.vcf"; 14 | #my $f_filter_out=$run_dir."/mutect/mutect.filtered.vcf"; 15 | 16 | ### minimum vaf for tumor 0.05, column 10 ### 17 | ## maximum vaf for normal 0.02, column 11 ### 18 | 19 | ### get the bam path ## 20 | my @temp=split(/\//,$f_m); 21 | 22 | my $path_d="/"; 23 | 24 | for(my $i=1;$i; 104 | my $min_vaf_somatic=$minvaf; 105 | my $max_vaf_germline=0.02; 106 | #my $min_coverage=$mincov; 107 | my $tumor_normal_order=-1; 108 | 109 | open(IN,"<$f_m"); 110 | open(OUT,">$f_filter_out"); 111 | 112 | while() 113 | { 114 | my $l=$_; 115 | chomp($l); 116 | if($l=~/^#/) { #print OUT $l,"\n"; 117 | if($l=~/^#CHROM/) { 118 | my @temphead=split("\t",$l); 119 | print OUT $temphead[0]; 120 | for(my $i=1;$i<=8;$i++) 121 | { 122 | print OUT "\t",$temphead[$i]; 123 | } 124 | 125 | if($temphead[9] eq $sn_t && $temphead[10] eq $sn_n) { print OUT "\t","TUMOR","\t","NORMAL","\n"; $tumor_normal_order=1; } 126 | if($temphead[9] eq $sn_n && $temphead[10] eq $sn_t) { print OUT "\t","NORMAL","\t","TUMOR","\n"; $tumor_normal_order=0; } 127 | } 128 | else { print OUT $l,"\n"; } 129 | } 130 | 131 | else { 132 | #print $tumor_normal_order,"\n"; 133 | #; 134 | my @temp=split("\t",$l); 135 | if($tumor_normal_order==-1) { last; } 136 | my $tumor=$temp[9]; 137 | my $normal=$temp[10]; 138 | 139 | if($tumor_normal_order==0) { 140 | $tumor=$temp[10]; 141 | $normal=$temp[9]; 142 | } 143 | 144 | my @tempt=split(":",$tumor); 145 | my @tempn=split(":",$normal); 146 | my @readt=split(",",$tempt[1]); 147 | my @readn=split(",",$tempn[1]); 148 | 149 | #print $l,"\n"; 150 | #print $readn[0], "\t", $readn[1],"\n"; 151 | #; 152 | #print $readt[0], "\t", $readt[1],"\n"; 153 | 154 | #### readn[0]: read count for ref allele in normal ## 155 | ### readn[1]: read count for alt allele in normal ## 156 | #### readt[0]: read count for ref allele in tumor ## 157 | ### readt[1]: read count for alt allele in tumor ## 158 | 159 | my $tot_n=$readn[0]+$readn[1]; 160 | my $tot_t=$readt[0]+$readt[1]; 161 | 162 | if($tot_n==0 || $tot_t==0) { next; } 163 | 164 | my $vaf_t=$readt[1]/$tot_t; 165 | my $vaf_n=$readn[1]/$tot_n; 166 | #print $vaf_t,"\t",$vaf_n,"\n"; 167 | ## apply filtering ## 168 | if($temp[6] eq "PASS" && $vaf_t>=$min_vaf_somatic && $vaf_n<=$max_vaf_germline && $tot_n>=$mincov_n && $tot_t>=$mincov_t) 169 | { 170 | print OUT $l,"\n"; 171 | } 172 | } 173 | 174 | } 175 | 176 | 177 | -------------------------------------------------------------------------------- /filter_mutect1.8.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## normal <=2% 4 | ### mutect1.8 filtering ### 5 | 6 | ## turn off minvaf cut-off, Apr 20, 2020 ## 7 | 8 | use strict; 9 | use warnings; 10 | die unless @ARGV == 6; 11 | ### samtools ## 12 | 13 | my ($samtools,$f_m,$f_filter_out,$mincov_t,$mincov_n,$minvaf)=@ARGV; 14 | 15 | #my $f_m=$run_dir."/mutect/mutect.raw.vcf"; 16 | #my $f_filter_out=$run_dir."/mutect/mutect.filtered.vcf"; 17 | 18 | ### minimum vaf for tumor 0.05, column 10 ### 19 | ## maximum vaf for normal 0.02, column 11 ### 20 | 21 | ## turn off minvaf cut-off ## 22 | 23 | ### get the bam path ## 24 | 25 | my @temp=split(/\//,$f_m); 26 | 27 | my $path_d="/"; 28 | 29 | for(my $i=1;$i; 109 | my $min_vaf_somatic=$minvaf; 110 | my $max_vaf_germline=0.02; 111 | #my $min_coverage=$mincov; 112 | my $tumor_normal_order=-1; 113 | 114 | open(IN,"<$f_m"); 115 | open(OUT,">$f_filter_out"); 116 | 117 | while() 118 | { 119 | my $l=$_; 120 | chomp($l); 121 | if($l=~/^#/) { #print OUT $l,"\n"; 122 | if($l=~/^#CHROM/) { 123 | my @temphead=split("\t",$l); 124 | print OUT $temphead[0]; 125 | for(my $i=1;$i<=8;$i++) 126 | { 127 | print OUT "\t",$temphead[$i]; 128 | } 129 | 130 | if($temphead[9] eq $sn_t && $temphead[10] eq $sn_n) { print OUT "\t","TUMOR","\t","NORMAL","\n"; $tumor_normal_order=1; } 131 | if($temphead[9] eq $sn_n && $temphead[10] eq $sn_t) { print OUT "\t","NORMAL","\t","TUMOR","\n"; $tumor_normal_order=0; } 132 | } 133 | else { print OUT $l,"\n"; } 134 | } 135 | 136 | else { 137 | #print $tumor_normal_order,"\n"; 138 | #; 139 | my @temp=split("\t",$l); 140 | if($tumor_normal_order==-1) { last; } 141 | my $tumor=$temp[9]; 142 | my $normal=$temp[10]; 143 | 144 | if($tumor_normal_order==0) { 145 | $tumor=$temp[10]; 146 | $normal=$temp[9]; 147 | } 148 | 149 | my @tempt=split(":",$tumor); 150 | my @tempn=split(":",$normal); 151 | my @readt=split(",",$tempt[1]); 152 | my @readn=split(",",$tempn[1]); 153 | 154 | #print $l,"\n"; 155 | #print $readn[0], "\t", $readn[1],"\n"; 156 | #; 157 | #print $readt[0], "\t", $readt[1],"\n"; 158 | 159 | #### readn[0]: read count for ref allele in normal ## 160 | ### readn[1]: read count for alt allele in normal ## 161 | #### readt[0]: read count for ref allele in tumor ## 162 | ### readt[1]: read count for alt allele in tumor ## 163 | 164 | my $tot_n=$readn[0]+$readn[1]; 165 | my $tot_t=$readt[0]+$readt[1]; 166 | 167 | if($tot_n==0 || $tot_t==0) { next; } 168 | 169 | my $vaf_t=$readt[1]/$tot_t; 170 | my $vaf_n=$readn[1]/$tot_n; 171 | #print $vaf_t,"\t",$vaf_n,"\n"; 172 | ## apply filtering ## 173 | if($temp[6] eq "PASS" && $vaf_n<=$max_vaf_germline && $tot_n>=$mincov_n && $tot_t>=$mincov_t) 174 | { 175 | print OUT $l,"\n"; 176 | } 177 | } 178 | 179 | } 180 | 181 | 182 | -------------------------------------------------------------------------------- /generate_coding_report.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ### for example, 4 | use strict; 5 | use warnings; 6 | die unless @ARGV == 2; 7 | my ($f_in, $f_out)=@ARGV; 8 | 9 | open(OUT,">$f_out"); 10 | my %count_v; 11 | my $f_status=$f_out.".status\n"; 12 | 13 | open(OUT1,">$f_status"); 14 | 15 | foreach my $l (`cat $f_in`) 16 | { 17 | my $ltr=$l; 18 | chomp($ltr); 19 | if($ltr=~/^#version/) { next; } 20 | else { 21 | if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; next; } 22 | else { 23 | my @temp=split("\t",$ltr); 24 | my $annot=$temp[8]; 25 | my $sn=$temp[15]; 26 | $sn=~s/_T//g; 27 | if($annot=~/Frame_Shift_Del/ || $annot=~/Frame_Shift_Ins/ || $annot=~/Missense_Mutation/ || $annot=~/Nonsense_Mutation/ || $annot=~/Nonstop_Mutation/ || $annot=~/Silent/ || $annot=~/Splice_Site/ || $annot=~/In_Frame_Ins/ || $annot=~/In_Frame_Del/) { 28 | print OUT $ltr,"\n"; 29 | $count_v{$sn}++; 30 | } 31 | } 32 | } 33 | } 34 | 35 | close OUT; 36 | 37 | foreach my $s (sort keys %count_v) 38 | { 39 | print OUT1 $s,"\t",$count_v{$s},"\n"; 40 | } 41 | 42 | close OUT1; 43 | -------------------------------------------------------------------------------- /generate_final_report.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ### for example, 4 | ## tumor >= 5% and normal <=1% 5 | use strict; 6 | use warnings; 7 | die unless @ARGV == 2; 8 | my ($run_dir, $s_exonic)=@ARGV; 9 | 10 | my $working_name= (split(/\//,$run_dir))[-1]; 11 | 12 | my $f_sum=$run_dir."/".$working_name.".withmutect.maf\n"; 13 | my $f_status=$run_dir."/".$working_name.".withmutect.status\n"; 14 | 15 | open(OUT1,">$f_sum"); 16 | open(OUT2,">$f_status"); 17 | 18 | my $head_w=0; 19 | 20 | foreach my $d (`ls $run_dir`) 21 | { 22 | my $dtr=$d; 23 | chomp($dtr); 24 | 25 | # my $f_maf=$run_dir."/".$dtr."/".$dtr.".checked.maf"; 26 | my $f_maf=$run_dir."/".$dtr."/".$dtr.".withmutect.filtered.maf"; 27 | if(-e $f_maf) 28 | { 29 | my $count=0; 30 | foreach my $l (`cat $f_maf`) 31 | { 32 | my $ltr=$l; 33 | chomp($ltr); 34 | if($ltr=~/^#version/) { next; } 35 | else { 36 | if($ltr=~/^Hugo/) { if($head_w==0) { print OUT1 $ltr,"\n"; } $head_w=1; } 37 | else { 38 | my @temp=split("\t",$ltr); 39 | my $annot=$temp[8]; 40 | my $af=$temp[99]; 41 | #if($annot=~/Frame_Shift_Del/ || $annot=~/Frame_Shift_Ins/ || $annot=~/Missense_Mutation/ || $annot=~/Nonsense_Mutation/ || $annot=~/Nonstop_Mutation/ || $annot=~/Silent/ || $annot=~/Splice_Site/ || $annot=~/In_Frame_Ins/ || $annot=~/In_Frame_Del/ || $s_exonic==0) { 42 | #if($af eq "" || (($af ne "") && $af<0.005)) 43 | #{ 44 | if(1==1) 45 | { 46 | print OUT1 $ltr,"\n"; 47 | $count++; 48 | #} 49 | } 50 | } 51 | } 52 | } 53 | print OUT2 $count,"\t",$f_maf,"\n"; 54 | } 55 | 56 | } ## 57 | 58 | 59 | close OUT1; 60 | close OUT2; 61 | 62 | -------------------------------------------------------------------------------- /generate_maf.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | use warnings; 5 | 6 | my @dir=("/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/CO", "/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/CO2", "/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/BRCA2", "/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/BRCA3", "/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/OV"); 7 | #my @dir=("/gscuser/scao/gc2521/dinglab/cptac_prospective_samples/exome/somatic/CO2"); 8 | 9 | my $tool_dir="/gscmnt/gc2741/ding/qgao/tools/vcf2maf-1.6.11"; 10 | foreach my $d (@dir) 11 | { 12 | # print "$d\n"; 13 | foreach my $s (glob("$d/*")) 14 | { 15 | my @samp = split(/\//,$s); 16 | system("ln -s $s/merged.vcf $samp[-1].vcf"); 17 | system("ln -s $s/merged.VEP.vcf $samp[-1].vep.vcf"); 18 | system("bsub -oo $samp[-1].log perl $tool_dir/vcf2maf.pl --input-vcf $samp[-1].vcf --output-maf $samp[-1].maf --tumor-id $samp[-1]\_T --normal-id $samp[-1]\_N --ref-fasta /gscuser/scao/gc3027/fasta/GRCh37V1/GRCh37-lite-chr_with_chrM.fa --filter-vcf $tool_dir/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz"); 19 | } 20 | } 21 | 22 | -------------------------------------------------------------------------------- /genomevip_label.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | # --------------------- 3 | # @name GenomeVIP utility to annotate with variant calling tool program 4 | # @author R. Jay Mashl 5 | # @version 6 | # 7 | # @syntax anno_genomevip.pl program_name source.vcf destination.vcf 8 | # --------------------- 9 | use strict; 10 | use warnings; 11 | 12 | my ($progid, $infile, $outfile, @header, $encoding, %assoc); 13 | 14 | 15 | $progid = $ARGV[0]; $infile = $ARGV[1]; $outfile = $ARGV[2]; 16 | %assoc = ("VarScan"=>1,"Pindel"=>2,"BreakDancer"=>3,"GenomeSTRiP"=>4,"Strelka"=>5,"GATK"=>6,"MuTect"=>7); 17 | $encoding="VarScan,1;Pindel,2;BreakDancer,3;GenomeSTRiP,4;Strelka,5;GATK,6;MuTect,7"; 18 | 19 | # Insert custom info line after last existing info line, then update info 20 | open (IN, "<", $infile) || die "Error: cannot open input file $infile"; close(IN); 21 | @header = `grep '^#' $infile`; 22 | my $idx=-1; 23 | for (my $i=scalar(@header)-1; $i>= 0; $i--) { 24 | if ($header[$i] =~ /^##INFO=/) { 25 | $idx = $i; 26 | last; 27 | } 28 | } 29 | open (OUT,">", $outfile) || die "Error: cannot open output file $outfile"; 30 | for (my $i=0; $i\n" if ($i==$idx); 33 | } 34 | open (IN, "<", $infile); 35 | while() { 36 | if($_ !~ /^#/) { 37 | chomp; 38 | my @a = split /\t/; 39 | $a[7] .= ";GENOMEVIP=". $assoc{$progid}; 40 | print OUT join("\t", @a)."\n"; 41 | } 42 | } 43 | close(IN); 44 | close(OUT); 45 | -------------------------------------------------------------------------------- /get_strelka_passed_snv_indel.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ### 10/10/2018 ## 4 | ### get passed snv and indel variants 5 | ### add the filtering for indel length ## 6 | 7 | use strict; 8 | use warnings; 9 | 10 | die unless @ARGV == 4; 11 | my ($f_snv_in,$f_indel_in,$f_snv_out,$f_indel_out)=@ARGV; 12 | 13 | open(OUT1,">$f_snv_out"); 14 | open(OUT2,">$f_indel_out"); 15 | my $head; 16 | #my $firsttime=1; 17 | 18 | foreach my $l (`zcat $f_snv_in`) 19 | { 20 | my $ltr=$l; 21 | chomp($ltr); 22 | if($ltr=~/^#/) { 23 | # if($ltr=~/^#CHROM/) 24 | # { 25 | # $head=$ltr; 26 | # } 27 | print OUT1 $ltr,"\n"; 28 | next; } 29 | else { 30 | my @temp=split("\t",$ltr); 31 | #my $ref=$temp[3]; 32 | #my $var=$temp[4]; 33 | if($temp[6] eq "PASS") 34 | { 35 | print OUT1 $ltr, "\n"; 36 | } 37 | } 38 | } 39 | foreach my $l (`zcat $f_indel_in`) 40 | { 41 | my $ltr=$l; 42 | chomp($ltr); 43 | if($ltr=~/^#/) { print OUT2 $ltr,"\n"; next; } 44 | else { 45 | my @temp=split("\t",$ltr); 46 | #my $ref=$temp[3]; 47 | #my $var=$temp[4]; 48 | if($temp[6] eq "PASS") 49 | { 50 | #if($firsttime==1) { print OUT2 $head,"\n"; $firsttime=0; } 51 | print OUT2 $ltr, "\n"; 52 | } 53 | } 54 | } 55 | 56 | close OUT1; 57 | close OUT2; 58 | 59 | -------------------------------------------------------------------------------- /merge_mutect.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | use warnings; 5 | die unless @ARGV == 1; 6 | 7 | ## merge calls from different chromosomes ## 8 | 9 | my @chrlist=("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y"); 10 | my ($sample_full_path)=@ARGV; 11 | my $f_snv; 12 | my $f_indel; 13 | 14 | my $f_snv_idx; 15 | my $f_indel_idx; 16 | 17 | my $f_raw; 18 | my $f_raw_idx; 19 | 20 | my $f_snv_out=$sample_full_path."/mutect1/mutect.filter.snv.vcf"; 21 | my $f_ind_out=$sample_full_path."/mutect1/mutect.filter.indel.vcf"; 22 | 23 | open(OUT1,">$f_snv_out"); 24 | open(OUT2,">$f_ind_out"); 25 | 26 | foreach my $chr (@chrlist) 27 | { 28 | 29 | $f_snv=$sample_full_path."/mutect1/mutect.filter.snv.$chr.vcf"; 30 | $f_indel=$sample_full_path."/mutect1/mutect.filter.indel.$chr.vcf"; 31 | 32 | $f_snv_idx=$sample_full_path."/mutect1/mutect.filter.snv.$chr.vcf.idx"; 33 | $f_indel_idx=$sample_full_path."/mutect1/mutect.filter.indel.$chr.vcf.idx";; 34 | 35 | $f_raw=$sample_full_path."/mutect1/mutect.raw.filtered.$chr.vcf"; 36 | $f_raw_idx=$sample_full_path."/mutect1/mutect.raw.filtered.$chr.vcf.idx"; 37 | #$f_raw_idx=$sample_full_path."/mutect/".$sample_name.".gvip.$chr.vcf.idx"; 38 | #$f_raw=$sample_full_path."/mutect/".$sample_name.".snv.gvip.$chr.vcf"; 39 | 40 | if(-e $f_snv) 41 | { 42 | foreach my $l (`cat $f_snv`) 43 | { 44 | my $ltr=$l; 45 | chomp($ltr); 46 | if($ltr=~/^#/ && !($chr eq "1")) { next; } 47 | else { print OUT1 $ltr,"\n"; } 48 | } 49 | `rm $f_snv`; 50 | `rm $f_snv_idx`; 51 | } 52 | 53 | if(-e $f_indel) 54 | { 55 | foreach my $l (`cat $f_indel`) 56 | { 57 | my $ltr=$l; 58 | chomp($ltr); 59 | if($ltr=~/^#/ && !($chr eq "1")) { next; } 60 | else { print OUT2 $ltr,"\n"; } 61 | } 62 | `rm $f_indel`; 63 | `rm $f_indel_idx`; 64 | } 65 | 66 | `rm $f_raw`; 67 | #`rm $f_raw`; 68 | #`rm $f_raw_idx`; 69 | `rm $f_raw_idx`; 70 | 71 | #print GATK "rawvcf=".$sample_full_path."/mutect/".$sample_name.".raw.$chr.vcf\n"; 72 | #print GATK "gvipvcf=".$sample_full_path."/mutect/".$sample_name.".gvip.$chr.vcf\n"; 73 | #print GATK "snvvcf=".$sample_full_path."/mutect/".$sample_name.".snv.gvip.$chr.vcf\n"; 74 | #print GATK "indelvcf=".$sample_full_path."/mutect/".$sample_name.".indel.gvip.$chr.vcf\n"; 75 | #print GATK " ".$run_script_path."genomevip_label.pl GATK \${rawvcf} \${gvipvcf}"."\n"; 76 | } 77 | -------------------------------------------------------------------------------- /qc_vcf.pl: -------------------------------------------------------------------------------- 1 | ######### Song Cao########### 2 | # qc_vcf.pl # 3 | 4 | #!/usr/bin/perl 5 | use strict; 6 | use warnings; 7 | 8 | die unless @ARGV == 2; 9 | 10 | my ($vcf_in,$vcf_out)=@ARGV; 11 | 12 | open(IN,"<$vcf_in"); 13 | open(OUT,">$vcf_out"); 14 | my @t; 15 | my $ref; 16 | my $var; 17 | while() 18 | { 19 | my $ltr=$_; 20 | chomp($ltr); 21 | if($ltr=~/^#/) 22 | { 23 | print OUT $ltr,"\n"; 24 | } 25 | else 26 | { 27 | @t=split("\t",$ltr); 28 | # filter case ref eq var ## 29 | $ref=$t[3]; 30 | $var=$t[4]; 31 | if($ref eq $var) 32 | { 33 | next; 34 | } 35 | else { print OUT $ltr,"\n"; } 36 | } 37 | } 38 | 39 | close IN; 40 | close OUT; 41 | #my @temp = split("/", $dir); 42 | #my $run_name = pop @temp; 43 | #my $f_out=$run_dir."/Analysis_Summary_Somatic_$run_name.tsv"; 44 | 45 | -------------------------------------------------------------------------------- /remove_largeindel.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | use strict; 4 | use warnings; 5 | die unless @ARGV == 2; 6 | my ($file_in,$file_out)=@ARGV; 7 | 8 | open(IN,"<$file_in"); 9 | open(OUT,">$file_out"); 10 | my @t; 11 | my $lref; 12 | my $lvar; 13 | while() 14 | { 15 | my $l=$_; 16 | chomp($l); 17 | if($l=~/^#/) { print OUT $l, "\n"; next; } 18 | else { 19 | @t=split("\t",$l); 20 | #$l=~s/SVTYPE=//g; 21 | $lref=length($t[3]); 22 | $lvar=length($t[4]); 23 | if(abs($lref-$lvar)<=100 && $lref<=101 && $lvar<=101) 24 | { 25 | print OUT $l,"\n"; 26 | } 27 | } 28 | } 29 | 30 | close IN; 31 | close OUT; 32 | -------------------------------------------------------------------------------- /remove_nearby_snv.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | 4 | ## Song Cao ## 5 | 6 | use strict; 7 | use warnings; 8 | 9 | die unless @ARGV == 2; 10 | 11 | ## chr: 4, pos 5, type 9, sn 15 starting from 0 ## 12 | 13 | ### 762 DEL 14 | ### 167 INS 15 | ## 7938 SNP ### 16 | 17 | my %ind=(); 18 | my %snv=(); 19 | my $window=20; 20 | 21 | my ($maf_in,$maf_out)=@ARGV; 22 | 23 | open(OUT,">$maf_out"); 24 | my $maf_out_rem=$maf_out.".removed"; 25 | open(OUT2,">$maf_out_rem"); 26 | 27 | foreach my $l (`cat $maf_in`) 28 | { 29 | my $ltr=$l; 30 | chomp($ltr); 31 | if($ltr=~/^Hugo/) { next; } 32 | else { 33 | my @temp=split("\t",$ltr); 34 | my $id=$temp[15]."_".$temp[4]; 35 | 36 | if($temp[9] eq "INS" || $temp[9] eq "DEL") 37 | { 38 | $ind{$id}{$temp[5]}=1; 39 | } 40 | 41 | if($temp[9] eq "SNP") 42 | { 43 | $snv{$id}{$temp[5]}=1; 44 | } 45 | 46 | } 47 | } 48 | 49 | foreach my $l (`cat $maf_in`) 50 | { 51 | my $ltr=$l; 52 | chomp($ltr); 53 | if($ltr=~/^Hugo/) { print OUT $ltr,"\n"; } 54 | else { 55 | my @temp=split("\t",$ltr); 56 | my $id=$temp[15]."_".$temp[4]; 57 | if($temp[9] eq "SNP") 58 | { 59 | my $remove_snv=0; 60 | if(defined $ind{$id}) 61 | { 62 | for(my $i=-$window;$i<=$window;$i++) 63 | { 64 | my $pos=$temp[5]+$i; 65 | if(defined $ind{$id}{$pos}) 66 | { 67 | $remove_snv=1; 68 | } 69 | } 70 | if($remove_snv==0) 71 | { 72 | print OUT $ltr,"\n"; 73 | } 74 | if($remove_snv==1) 75 | { 76 | print OUT2 $ltr,"\n"; 77 | } 78 | } 79 | else { print OUT $ltr,"\n"; } 80 | } 81 | else { print OUT $ltr,"\n"; } 82 | } 83 | } 84 | 85 | close OUT; 86 | close OUT2; 87 | -------------------------------------------------------------------------------- /set_envvars: -------------------------------------------------------------------------------- 1 | export PERL_PATH=/gsc 2 | export PATH=$PERL_PATH/bin:$PATH 3 | export PERL_BIN=$PERL_PATH/bin/perl 4 | export PERL5LIB=$PERL_PATH/lib/perl5/5.8.7/:$PERL5LIB 5 | -------------------------------------------------------------------------------- /snv_filter.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | #---------------------------------- 3 | # @name GenomeVIP SNVs false-positives filter using VarScan 4 | # @author Beifang Niu 5 | # @author R. Jay Mashl 6 | # @author song cao 7 | # @version 0.7 do not use tmp file: 8 | # @version 0.6 (rjm): make pass test explicit for extensibility 9 | # @version 0.5 (rjm): workaround for stat on AWS 10 | # @version 0.4 (rjm): handle zero-input case 11 | # @version 0.3 (rjm): adjust filenames and parameter names; allow for commented lines 12 | # @version 0.2 (rjm): added ENV and pass/fail splitter 13 | # @version 0.1 (bn): original 14 | #-------------------------------------- 15 | use strict; 16 | use warnings; 17 | 18 | use Cwd; 19 | use Carp; 20 | use FileHandle; 21 | use IO::File; 22 | use Getopt::Long; 23 | use POSIX qw( WIFEXITED ); 24 | use File::Temp qw/ tempfile /; 25 | #use File::stat; 26 | 27 | 28 | my $cmd; 29 | my $input_fh_passed; 30 | my $input_fh_failed; 31 | 32 | # get paras from config file 33 | my (%paras); 34 | map { chomp; if(!/^[#;]/ && /=/) { @_ = split /=/; $_[1] =~ s/ //g; my $v = $_[1]; print $v."\n"; $_[0] =~ s/ //g; $paras{ (split /\./, $_[0])[-1] } = $v } } (<>); 35 | # map { print; print "\t"; print $paras{$_}; print "\n" } keys %paras; 36 | # print $paras{'output'}."\n"; 37 | # 38 | print $paras{'variants_file'}."\n"; 39 | unless ( -e $paras{'variants_file'} ) { die "Variants input file could not be found !!! \n"; } 40 | 41 | # Create readcounts input 42 | my $input_fh = IO::File->new( $paras{'variants_file'} ) or die "Input variants file could not be opened."; 43 | my $read_count_input = $paras{'rc_in'}; 44 | 45 | my $read_count_input_fh = IO::File->new( $read_count_input, ">" ) or die "Temporary file could not be created. "; 46 | my %seen = (); 47 | map { unless( /^#/ ) { chomp; my @t = split /\t/; my $k = join( "\t", @t[0,1,1] ); $seen{$k} = 1;} } <$input_fh>; 48 | map { $read_count_input_fh->print($_."\n") } keys %seen; 49 | $input_fh->close || die "Error on closing input variants file"; 50 | 51 | # Run readcounts 52 | my $fs = `wc -l < $read_count_input`; 53 | if( $fs != 0) { 54 | 55 | my $read_count_output =$paras{'rc_out'}; 56 | 57 | #my ( undef, $read_count_output ) = tempfile(); 58 | my $cmd_run_read_count = "$paras{'bam_readcount'} -w 10 -l $read_count_input -q $paras{'min_mapping_qual'} -b $paras{'min_base_qual'} -f $paras{'REF'} $paras{'bam_file'} > $read_count_output"; 59 | print $cmd_run_read_count."\n"; 60 | system( $cmd_run_read_count ); 61 | my $fp_output_file = $paras{'fp_out'}; 62 | 63 | # my ( undef, $fp_output_file ) = tempfile(); 64 | my $cmd_run_varscan = "java $ENV{'JAVA_OPTS'} -jar $ENV{'VARSCAN_DIR'}/VarScan.jar fpfilter $paras{'variants_file'} $read_count_output --output-file $fp_output_file --keep-failures 1 --min-var-count $paras{'min_num_var_supporting_reads'} --min-var-freq $paras{'min_var_allele_freq'} --min-var-readpos $paras{'min_avg_rel_read_position'} --min-var-dist3 $paras{'min_avg_rel_dist_to_3prime_end'} --min-strandedness $paras{'min_var_strandedness'} --min-strand-reads $paras{'min_allele_depth_for_testing_strandedness'} --min-ref-basequal $paras{'min_ref_allele_avg_base_qual'} --min-var-basequal $paras{'min_var_allele_avg_base_qual'} --max-rl-diff $paras{'max_rel_read_length_difference'} --max-var-mmqs $paras{'max_mismatch_qual_sum_for_var_reads'} --max-mmqs-diff $paras{'max_avg_mismatch_qual_sum_difference'} --min-ref-mapqual $paras{'min_ref_allele_avg_mapping_qual'} --min-var-mapqual $paras{'min_var_allele_avg_mapping_qual'} --max-mapqual-diff $paras{'max_avg_mapping_qual_difference'} "; 65 | print $cmd_run_varscan."\n"; 66 | system( $cmd_run_varscan ); 67 | 68 | # (rjm) varscan --filtered-file option does not work at all, so manually extract failed calls 69 | $input_fh = IO::File->new( $fp_output_file , "r") or die "File for varscan fpfilter results could not be opened. "; 70 | $input_fh_passed = IO::File->new( $paras{'passfile'}, "w") or die "could not open file for writing passed variants. "; 71 | $input_fh_failed = IO::File->new( $paras{'failfile'}, "w") or die "could not open file for writing failed variants. "; 72 | while (<$input_fh>) { 73 | if( /^#/ ) { 74 | $input_fh_passed->print($_); 75 | $input_fh_failed->print($_); 76 | } else { 77 | my @a = split /\t/; 78 | if ( $a[6] eq "PASS" || $a[6] eq "." ) { # dot option is for gatk 79 | $input_fh_passed->print($_); 80 | } else { 81 | $input_fh_failed->print($_); 82 | } 83 | } 84 | } 85 | $input_fh_failed->close || die "Error on closing failed calls file"; 86 | $input_fh_passed->close || die "Error on closing passed calls file"; 87 | $input_fh->close || die "Error on closing input variants file"; 88 | #$cmd="rm -f $read_count_input $read_count_output $fp_output_file"; 89 | #print $cmd."\n"; 90 | # system( $cmd ); 91 | 92 | } else { 93 | 94 | print "# NOTICE: no variants are available for performing readcounts!\n"; 95 | $input_fh = IO::File->new( $paras{'variants_file'} ) or die "Input variants file could not be opened."; 96 | $input_fh_passed = IO::File->new( $paras{'passfile'}, "w") or die "could not open file for writing passed variants. "; 97 | $input_fh_failed = IO::File->new( $paras{'failfile'}, "w") or die "could not open file for writing failed variants. "; 98 | while (<$input_fh>) { 99 | if( /^#/ ) { 100 | $input_fh_passed->print($_); 101 | $input_fh_failed->print($_); 102 | } 103 | } 104 | $input_fh_failed->close || die "Error on closing failed calls file"; 105 | $input_fh_passed->close || die "Error on closing passed calls file"; 106 | $input_fh->close || die "Error on closing input variants file"; 107 | 108 | } 109 | 110 | 111 | 1; 112 | -------------------------------------------------------------------------------- /splice_site_check.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | ### check splice_site if it is correctly annotated ### 3 | use strict; 4 | use warnings; 5 | die unless @ARGV == 1; 6 | my ($run_dir)=@ARGV; 7 | 8 | my $sn=(split(/\//,$run_dir))[-1]; 9 | 10 | my %splice_s=(); 11 | 12 | my $f_bed="/gscmnt/gc2524/dinglab/bed_maker/E75_bed_v3.tsv"; 13 | my $f_in=$run_dir."/".$sn.".maf"; 14 | my $f_out=$run_dir."/".$sn.".checked.maf"; 15 | 16 | open(IN,"<$f_bed"); 17 | open(OUT,">$f_out"); 18 | 19 | while() 20 | { 21 | my $l=$_; 22 | chomp($l); 23 | my @temp=split("\t",$l); 24 | my $chr=$temp[0]; 25 | $chr=~s/chr//g; 26 | my $p1=$temp[1]+1; 27 | my $p2=$temp[2]+1; 28 | my $p3=$p1+1; 29 | my $p4=$p2-1; 30 | my @inf=split(":",$temp[3]); 31 | my $intron=$inf[3]; 32 | if($intron=~/^i/) { 33 | my $site1=$chr.":".$p1; 34 | my $site2=$chr.":".$p2; 35 | my $site3=$chr.":".$p3; 36 | my $site4=$chr.":".$p4; 37 | 38 | $splice_s{$site1}=1; 39 | $splice_s{$site2}=1; 40 | $splice_s{$site3}=1; 41 | $splice_s{$site4}=1; 42 | 43 | } 44 | } 45 | 46 | foreach my $l (`cat $f_in`) 47 | { 48 | my $ltr=$l; 49 | chomp($ltr); 50 | if($ltr=~/^Hugo/ || $ltr=~/version 2\.4/) { print OUT $ltr,"\n"; } 51 | else { 52 | my @temp=split("\t",$ltr); 53 | # print $temp[8],"\n"; 54 | if($temp[8] eq "Intron") 55 | { 56 | my $chr=$temp[4]; 57 | my $type=$temp[9]; 58 | $chr=~s/chr//g; 59 | my $ref=$temp[10]; 60 | my $var=$temp[12]; 61 | my $pos=$temp[5]; 62 | if($type eq "SNP") 63 | { 64 | my $p1=$chr.":".$pos; 65 | if(defined $splice_s{$p1}) 66 | { 67 | $ltr=~s/Intron/Splice_Site/g; 68 | } 69 | print OUT $ltr,"\n"; 70 | } 71 | elsif($type eq "DEL") 72 | { 73 | for(my $i=0;$i= 5% and normal <=1% 4 | ### add the filtering for indel length ## 5 | 6 | use strict; 7 | use warnings; 8 | die unless @ARGV == 1; 9 | my ($run_dir)=@ARGV; 10 | 11 | my $f_m=$run_dir."/merged.vcf"; 12 | my $f_filter_out=$run_dir."/merged.filtered.vcf"; 13 | my $f_vaf_out=$run_dir."/merged.vaf"; 14 | my $min_vaf_somatic=0.05; 15 | my $max_vaf_germline=0.02; 16 | my $min_coverage=20; 17 | 18 | open(OUT1,">$f_filter_out"); 19 | open(OUT2,">$f_vaf_out"); 20 | 21 | foreach my $l (`cat $f_m`) 22 | { 23 | my $ltr=$l; 24 | chomp($ltr); 25 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 26 | else { 27 | my @temp=split("\t",$ltr); 28 | #my $ref=$temp[3]; 29 | #my $var=$temp[4]; 30 | 31 | 32 | my $info=$temp[7]; 33 | my @temp2; 34 | my %rc; 35 | my %rc2; 36 | my $r_tot; 37 | my $r_tot2; 38 | my $vaf_n; 39 | my $vaf_t; 40 | my $ref; 41 | my $var; 42 | my $nt; 43 | my $ndp_ref; 44 | my $ndp_var; 45 | my $tdp_ref; 46 | my $tdp_var; 47 | 48 | $ref=$temp[3]; 49 | $var=$temp[4]; 50 | 51 | if(length($ref)>=20 || length($var)>=20) { next; } 52 | 53 | if($info=~/strelka/) 54 | { 55 | #print $info,"\n"; 56 | #; 57 | 58 | $vaf_n=$temp[11]; 59 | $vaf_t=$temp[12]; 60 | $ref=$temp[3]; 61 | $var=$temp[4]; 62 | $r_tot=0; 63 | 64 | @temp2=split(":",$vaf_n); 65 | %rc=(); 66 | #print $vaf_n,"\n"; 67 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 68 | #; 69 | #my @temp3=split(",",$temp2[0]); 70 | #$rc{'A'}=$temp3[0]; 71 | 72 | $rc{'A'}=(split(",",$temp2[0]))[0]; 73 | $rc{'C'}=(split(",",$temp2[1]))[0]; 74 | $rc{'G'}=(split(",",$temp2[4]))[0]; 75 | $rc{'T'}=(split(",",$temp2[7]))[0]; 76 | #print $vaf_n,"\n"; 77 | #print $vaf_t,"\n"; 78 | #; 79 | foreach my $nt (keys %rc) 80 | { 81 | $r_tot+=$rc{$nt}; 82 | #print $rc{$nt},"\n"; 83 | } 84 | 85 | @temp2=split(":",$vaf_t); 86 | 87 | %rc2=(); 88 | 89 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 90 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 91 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 92 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 93 | 94 | foreach $nt (sort keys %rc2) 95 | { 96 | $r_tot2+=$rc2{$nt}; 97 | #print $rc2{$nt},"\n"; 98 | } 99 | #print $ltr,"\n"; 100 | my @vars=split(",",$var); 101 | my $rcvar=0; 102 | my $rc2var=0; 103 | foreach my $v (@vars) 104 | { 105 | $rcvar+=$rc{$v}; 106 | $rc2var+=$rc2{$v}; 107 | } 108 | 109 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 110 | #; 111 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 112 | 113 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 114 | { 115 | print OUT1 $ltr,"\n"; 116 | } 117 | } 118 | 119 | elsif($info=~/varscan/ || $info=~/varindel/) 120 | { 121 | $vaf_n=$temp[11]; 122 | $vaf_t=$temp[12]; 123 | @temp2=split(":",$vaf_n); 124 | #print $vaf_n,"\n"; 125 | my @ndp4=split(",",$temp2[3]); 126 | 127 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 128 | $ndp_ref=$ndp4[0]+$ndp4[1]; 129 | $ndp_var=$ndp4[2]+$ndp4[3]; 130 | #print $vaf_t,"\n"; 131 | @temp2=split(":",$vaf_t); 132 | my @tdp4=split(",",$temp2[3]); 133 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 134 | 135 | $tdp_ref=$tdp4[0]+$tdp4[1]; 136 | $tdp_var=$tdp4[2]+$tdp4[3]; 137 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 138 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 139 | { 140 | print OUT1 $ltr,"\n"; 141 | } 142 | } 143 | 144 | elsif($info=~/pindel/) 145 | { 146 | 147 | $vaf_t=$temp[10]; 148 | $vaf_n=$temp[9]; 149 | if(!($vaf_t=~/\:/)) { next; } 150 | if(!($vaf_n=~/\:/)) { next; } 151 | 152 | @temp2=split(":",$vaf_n); 153 | my @ndp2=split(",",$temp2[1]); 154 | $ndp_ref=$ndp2[0]; 155 | $ndp_var=$ndp2[1]; 156 | @temp2=split(":",$vaf_t); 157 | my @tdp2=split(",",$temp2[1]); 158 | $tdp_ref=$tdp2[0]; 159 | $tdp_var=$tdp2[1]; 160 | #print $ndp_ref,"\t",$ndp_var,"\t",$tdp_ref,"\t",$tdp_var,"\n"; 161 | #; 162 | 163 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 164 | 165 | if($tdp_var/($tdp_var+$tdp_ref)>=$min_vaf_somatic && $ndp_var/($ndp_ref+$ndp_var)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 166 | { 167 | #print $ltr,"\n"; 168 | print OUT1 $ltr,"\n"; 169 | } 170 | 171 | } 172 | 173 | 174 | } 175 | } 176 | -------------------------------------------------------------------------------- /vaf_filter_hg19.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | use strict; 5 | use warnings; 6 | die unless @ARGV == 1; 7 | my ($run_dir)=@ARGV; 8 | 9 | my $f_m=$run_dir."/merged.vcf"; 10 | my $f_filter_out=$run_dir."/merged.filtered.vcf"; 11 | my $f_vaf_out=$run_dir."/merged.vaf"; 12 | my $min_vaf_somatic=0.05; 13 | my $max_vaf_germline=0.02; 14 | my $min_coverage=20; 15 | 16 | open(OUT1,">$f_filter_out"); 17 | open(OUT2,">$f_vaf_out"); 18 | 19 | foreach my $l (`cat $f_m`) 20 | { 21 | my $ltr=$l; 22 | chomp($ltr); 23 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 24 | else { 25 | my @temp=split("\t",$ltr); 26 | my $info=$temp[7]; 27 | my @temp2; 28 | my %rc; 29 | my %rc2; 30 | my $r_tot; 31 | my $r_tot2; 32 | my $vaf_n; 33 | my $vaf_t; 34 | my $ref; 35 | my $var; 36 | my $nt; 37 | my $ndp_ref; 38 | my $ndp_var; 39 | my $tdp_ref; 40 | my $tdp_var; 41 | 42 | $ref=$temp[3]; 43 | $var=$temp[4]; 44 | 45 | if(length($ref)>=100 || length($var)>=100) { next; } 46 | 47 | if($info=~/strelka/) 48 | { 49 | #print $info,"\n"; 50 | #; 51 | 52 | $vaf_n=$temp[9]; 53 | $vaf_t=$temp[12]; 54 | $ref=$temp[3]; 55 | $var=$temp[4]; 56 | $r_tot=0; 57 | 58 | @temp2=split(":",$vaf_n); 59 | %rc=(); 60 | #print $vaf_n,"\n"; 61 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 62 | #; 63 | #my @temp3=split(",",$temp2[0]); 64 | #$rc{'A'}=$temp3[0]; 65 | 66 | $rc{'A'}=(split(",",$temp2[0]))[0]; 67 | $rc{'C'}=(split(",",$temp2[1]))[0]; 68 | $rc{'G'}=(split(",",$temp2[4]))[0]; 69 | $rc{'T'}=(split(",",$temp2[7]))[0]; 70 | #print $vaf_n,"\n"; 71 | #print $vaf_t,"\n"; 72 | #; 73 | foreach my $nt (keys %rc) 74 | { 75 | $r_tot+=$rc{$nt}; 76 | #print $rc{$nt},"\n"; 77 | } 78 | 79 | @temp2=split(":",$vaf_t); 80 | 81 | %rc2=(); 82 | 83 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 84 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 85 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 86 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 87 | 88 | foreach $nt (sort keys %rc2) 89 | { 90 | $r_tot2+=$rc2{$nt}; 91 | #print $rc2{$nt},"\n"; 92 | } 93 | #print $ltr,"\n"; 94 | my @vars=split(",",$var); 95 | my $rcvar=0; 96 | my $rc2var=0; 97 | foreach my $v (@vars) 98 | { 99 | $rcvar+=$rc{$v}; 100 | $rc2var+=$rc2{$v}; 101 | } 102 | 103 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 104 | #; 105 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 106 | 107 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 108 | { 109 | print OUT1 $ltr,"\n"; 110 | } 111 | } 112 | 113 | elsif($info=~/varscan/ || $info=~/varindel/) 114 | { 115 | $vaf_n=$temp[9]; 116 | $vaf_t=$temp[12]; 117 | @temp2=split(":",$vaf_n); 118 | #print $vaf_n,"\n"; 119 | my @ndp4=split(",",$temp2[3]); 120 | 121 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 122 | $ndp_ref=$ndp4[0]+$ndp4[1]; 123 | $ndp_var=$ndp4[2]+$ndp4[3]; 124 | #print $vaf_t,"\n"; 125 | @temp2=split(":",$vaf_t); 126 | my @tdp4=split(",",$temp2[3]); 127 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 128 | 129 | $tdp_ref=$tdp4[0]+$tdp4[1]; 130 | $tdp_var=$tdp4[2]+$tdp4[3]; 131 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 132 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 133 | { 134 | print OUT1 $ltr,"\n"; 135 | } 136 | } 137 | 138 | elsif($info=~/pindel/) 139 | { 140 | 141 | $vaf_n=$temp[10]; 142 | $vaf_t=$temp[11]; 143 | if(!($vaf_t=~/\:/)) { next; } 144 | if(!($vaf_n=~/\:/)) { next; } 145 | 146 | @temp2=split(":",$vaf_n); 147 | my @ndp2=split(",",$temp2[1]); 148 | $ndp_ref=$ndp2[0]; 149 | $ndp_var=$ndp2[1]; 150 | @temp2=split(":",$vaf_t); 151 | my @tdp2=split(",",$temp2[1]); 152 | $tdp_ref=$tdp2[0]; 153 | $tdp_var=$tdp2[1]; 154 | #print $ndp_ref,"\t",$ndp_var,"\t",$tdp_ref,"\t",$tdp_var,"\n"; 155 | #; 156 | 157 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 158 | 159 | if($tdp_var/($tdp_var+$tdp_ref)>=$min_vaf_somatic && $ndp_var/($ndp_ref+$ndp_var)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 160 | { 161 | print OUT1 $ltr,"\n"; 162 | } 163 | 164 | } 165 | 166 | 167 | } 168 | } 169 | -------------------------------------------------------------------------------- /vaf_filter_hg19_v1.1.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | use strict; 5 | use warnings; 6 | die unless @ARGV == 1; 7 | my ($run_dir)=@ARGV; 8 | 9 | my $f_m=$run_dir."/merged.vcf"; 10 | my $f_filter_out=$run_dir."/merged.filtered.vcf"; 11 | my $f_vaf_out=$run_dir."/merged.vaf"; 12 | my $min_vaf_somatic=0.05; 13 | my $min_vaf_pindel=0.1; 14 | my $max_vaf_germline=0.02; 15 | my $min_coverage=20; 16 | 17 | open(OUT1,">$f_filter_out"); 18 | open(OUT2,">$f_vaf_out"); 19 | 20 | foreach my $l (`cat $f_m`) 21 | { 22 | my $ltr=$l; 23 | chomp($ltr); 24 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 25 | else { 26 | my @temp=split("\t",$ltr); 27 | my $info=$temp[7]; 28 | my @temp2; 29 | my %rc; 30 | my %rc2; 31 | my $r_tot; 32 | my $r_tot2; 33 | my $vaf_n; 34 | my $vaf_t; 35 | my $ref; 36 | my $var; 37 | my $nt; 38 | my $ndp_ref; 39 | my $ndp_var; 40 | my $tdp_ref; 41 | my $tdp_var; 42 | 43 | $ref=$temp[3]; 44 | $var=$temp[4]; 45 | 46 | if(length($ref)>=100 || length($var)>=100) { next; } 47 | 48 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 49 | { 50 | $vaf_n=$temp[9]; 51 | $vaf_t=$temp[12]; 52 | $ref=$temp[3]; 53 | $var=$temp[4]; 54 | $r_tot=0; 55 | 56 | @temp2=split(":",$vaf_n); 57 | %rc=(); 58 | #print $vaf_n,"\n"; 59 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 60 | #; 61 | #my @temp3=split(",",$temp2[0]); 62 | #$rc{'A'}=$temp3[0]; 63 | $rc{'A'}=(split(",",$temp2[0]))[0]; 64 | $rc{'C'}=(split(",",$temp2[1]))[0]; 65 | $rc{'G'}=(split(",",$temp2[4]))[0]; 66 | $rc{'T'}=(split(",",$temp2[7]))[0]; 67 | #print $vaf_n,"\n"; 68 | #print $vaf_t,"\n"; 69 | #; 70 | foreach my $nt (keys %rc) 71 | { 72 | $r_tot+=$rc{$nt}; 73 | #print $rc{$nt},"\n"; 74 | } 75 | 76 | @temp2=split(":",$vaf_t); 77 | 78 | #print "1:\n"; 79 | #print $ltr,"\n"; 80 | 81 | %rc2=(); 82 | 83 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 84 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 85 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 86 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 87 | 88 | foreach $nt (sort keys %rc2) 89 | { 90 | $r_tot2+=$rc2{$nt}; 91 | #print $rc2{$nt},"\n"; 92 | } 93 | #print $ltr,"\n"; 94 | my @vars=split(",",$var); 95 | my $rcvar=0; 96 | my $rc2var=0; 97 | foreach my $v (@vars) 98 | { 99 | $rcvar+=$rc{$v}; 100 | $rc2var+=$rc2{$v}; 101 | } 102 | 103 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 104 | #; 105 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 106 | 107 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 108 | { 109 | print OUT1 $ltr,"\n"; 110 | } 111 | } 112 | 113 | elsif($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-mindel/) 114 | { 115 | $vaf_n=$temp[9]; 116 | $vaf_t=$temp[12]; 117 | @temp2=split(":",$vaf_n); 118 | #print $vaf_n,"\n"; 119 | #print "2:\n"; 120 | #print $ltr,"\n"; 121 | 122 | my @ndp4=split(",",$temp2[3]); 123 | 124 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 125 | $ndp_ref=$ndp4[0]+$ndp4[1]; 126 | $ndp_var=$ndp4[2]+$ndp4[3]; 127 | #print $vaf_t,"\n"; 128 | @temp2=split(":",$vaf_t); 129 | my @tdp4=split(",",$temp2[3]); 130 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 131 | 132 | $tdp_ref=$tdp4[0]+$tdp4[1]; 133 | $tdp_var=$tdp4[2]+$tdp4[3]; 134 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 135 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_pindel && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 136 | { 137 | $ltr=~s/SVTYPE=//g; 138 | print OUT1 $ltr,"\n"; 139 | } 140 | } 141 | 142 | elsif($info=~/set\=pindel-varindel/ || $info=~/set\=pindel-mindel/) 143 | { 144 | 145 | $vaf_n=$temp[10]; 146 | $vaf_t=$temp[11]; 147 | if(!($vaf_t=~/\:/)) { next; } 148 | if(!($vaf_n=~/\:/)) { next; } 149 | 150 | @temp2=split(":",$vaf_n); 151 | my @ndp2=split(",",$temp2[1]); 152 | $ndp_ref=$ndp2[0]; 153 | $ndp_var=$ndp2[1]; 154 | @temp2=split(":",$vaf_t); 155 | my @tdp2=split(",",$temp2[1]); 156 | $tdp_ref=$tdp2[0]; 157 | $tdp_var=$tdp2[1]; 158 | #print $ltr,"\n"; 159 | #print $ndp_ref,"\t",$ndp_var,"\t",$tdp_ref,"\t",$tdp_var,"\n"; 160 | #; 161 | 162 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 163 | 164 | if($tdp_var/($tdp_var+$tdp_ref)>=$min_vaf_somatic && $ndp_var/($ndp_ref+$ndp_var)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 165 | { 166 | $ltr=~s/SVTYPE=//g; 167 | print OUT1 $ltr,"\n"; 168 | } 169 | 170 | } 171 | 172 | 173 | } 174 | } 175 | -------------------------------------------------------------------------------- /vaf_filter_michigan_washu.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | 5 | ### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ## 6 | 7 | ### add the filtering for indel length ## 8 | 9 | use strict; 10 | use warnings; 11 | die unless @ARGV == 1; 12 | my ($run_dir)=@ARGV; 13 | 14 | my $f_m=$run_dir."/merged.withmutect.vcf"; 15 | my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf"; 16 | my $f_vaf_out=$run_dir."/merged.withmutect.vaf"; 17 | my $min_vaf_somatic=0.05; 18 | #my $min_vaf_pindel=0.1; 19 | my $max_vaf_germline=0.02; 20 | my $min_coverage=20; 21 | my $indel_max_size=100; 22 | 23 | open(OUT1,">$f_filter_out"); 24 | open(OUT2,">$f_vaf_out"); 25 | 26 | foreach my $l (`cat $f_m`) 27 | { 28 | my $ltr=$l; 29 | chomp($ltr); 30 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 31 | else { 32 | my @temp=split("\t",$ltr); 33 | #my $ref=$temp[3]; 34 | #my $var=$temp[4]; 35 | 36 | my $info=$temp[7]; 37 | my @temp2; 38 | my %rc; 39 | my %rc2; 40 | my $r_tot; 41 | my $r_tot2; 42 | my $vaf_n; 43 | my $vaf_t; 44 | my $ref; 45 | my $var; 46 | my $nt; 47 | my $ndp_ref; 48 | my $ndp_var; 49 | my $tdp_ref; 50 | my $tdp_var; 51 | 52 | $ref=$temp[3]; 53 | $var=$temp[4]; 54 | 55 | if(length($ref)>=$indel_max_size || length($var)>=$indel_max_size) { next; } 56 | 57 | #if($info=~/strelka-varscan/) and strelka-mutect ## 58 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/ ## 59 | if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 60 | # if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 61 | { 62 | 63 | #print $info,"\n"; 64 | #; 65 | #print $ltr,"\n"; 66 | 67 | $vaf_n=$temp[9]; 68 | $vaf_t=$temp[10]; 69 | $ref=$temp[3]; 70 | $var=$temp[4]; 71 | $r_tot=0; 72 | #print $ref,"\t",$var,"\n"; 73 | #print $vaf_n,"\n"; 74 | #print $vaf_t,"\n"; 75 | 76 | #; 77 | @temp2=split(":",$vaf_n); 78 | #%rc=(); 79 | #print $vaf_n,"\n"; 80 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 81 | #; 82 | #my @temp3=split(",",$temp2[0]); 83 | #$rc{'A'}=$temp3[0]; 84 | 85 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 86 | #...where: 87 | #ref_counts = value of FORMAT column value “TAR” 88 | #alt_counts = value of FORMAT column value “TIR” 89 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 90 | #alt_t1count = $alt_counts[0] (...likewise..) 91 | 92 | my $rcvar=(split(",",$temp2[-2]))[0]; 93 | my $rctot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 94 | my $rcref=$rctot-$rcvar; 95 | 96 | #$rc{'C'}=(split(",",$temp2[-2]))[0]; 97 | #print $vaf_n,"\n"; 98 | #print $vaf_t,"\n"; 99 | #; 100 | # foreach my $nt (keys %rc) 101 | # { 102 | # $r_tot+=$rc{$nt}; 103 | #print $rc{$nt},"\n"; 104 | # } 105 | 106 | @temp2=split(":",$vaf_t); 107 | 108 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 109 | #...where: 110 | #ref_counts = value of FORMAT column value “TAR” 111 | #alt_counts = value of FORMAT column value “TIR” 112 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 113 | #alt_t1count = $alt_counts[0] (...likewise..) 114 | 115 | my $rc2var=(split(",",$temp2[-2]))[0]; 116 | my $rc2tot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 117 | my $rc2ref=$rc2tot-$rc2var; 118 | 119 | #print $rcref,"\t",$rcvar,"\t",$rctot,"\n"; 120 | #print $rc2ref,"\t",$rc2var,"\t",$rc2tot,"\n"; 121 | #; 122 | 123 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 124 | #; 125 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rcref,"\t",$rcref/$rctot,"\t",$rcvar,"\t",$rcvar/$rctot,"\t",$rc2ref,"\t",$rc2ref/$rc2tot,"\t",$rc2var,"\t",$rc2var/$rc2tot,"\n"; 126 | 127 | if($rc2var/$rc2tot>=$min_vaf_somatic && $rcvar/$rctot<=$max_vaf_germline && $rc2tot>=$min_coverage && $rctot>=$min_coverage) 128 | { 129 | $ltr=~s/SVTYPE=//g; 130 | print OUT1 $ltr,"\n"; 131 | } 132 | } 133 | 134 | 135 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) for strelka 136 | 137 | #...where: 138 | 139 | #ref_counts = value of FORMAT column value “TAR” 140 | #alt_counts = value of FORMAT column value “TIR” 141 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 142 | #alt_t1count = $alt_counts[0] (...likewise..) 143 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 144 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 145 | { 146 | 147 | #print $info,"\n"; 148 | #; 149 | # print $ltr,"\n"; 150 | 151 | $vaf_n=$temp[9]; 152 | $vaf_t=$temp[10]; 153 | $ref=$temp[3]; 154 | $var=$temp[4]; 155 | $r_tot=0; 156 | # print $ref,"\t",$var,"\n"; 157 | # print $vaf_n,"\n"; 158 | # ; 159 | @temp2=split(":",$vaf_n); 160 | %rc=(); 161 | #print $vaf_n,"\n"; 162 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 163 | #; 164 | #my @temp3=split(",",$temp2[0]); 165 | #$rc{'A'}=$temp3[0]; 166 | 167 | #$rc{'A'}=(split(",",$temp2[0]))[0]; 168 | #$rc{'C'}=(split(",",$temp2[1]))[0]; 169 | #$rc{'G'}=(split(",",$temp2[4]))[0]; 170 | #$rc{'T'}=(split(",",$temp2[7]))[0]; 171 | $rc{'A'}=(split(",",$temp2[2]))[0]; 172 | $rc{'C'}=(split(",",$temp2[3]))[0]; 173 | $rc{'G'}=(split(",",$temp2[6]))[0]; 174 | $rc{'T'}=(split(",",$temp2[9]))[0]; 175 | #print $vaf_n,"\n"; 176 | #print $vaf_t,"\n"; 177 | #; 178 | foreach my $nt (keys %rc) 179 | { 180 | $r_tot+=$rc{$nt}; 181 | #print $rc{$nt},"\n"; 182 | } 183 | 184 | @temp2=split(":",$vaf_t); 185 | 186 | %rc2=(); 187 | 188 | $rc2{'A'}=(split(",",$temp2[2]))[0]; 189 | $rc2{'C'}=(split(",",$temp2[3]))[0]; 190 | $rc2{'G'}=(split(",",$temp2[6]))[0]; 191 | $rc2{'T'}=(split(",",$temp2[9]))[0]; 192 | 193 | foreach $nt (sort keys %rc2) 194 | { 195 | $r_tot2+=$rc2{$nt}; 196 | #print $rc2{$nt},"\n"; 197 | } 198 | #print $ltr,"\n"; 199 | my @vars=split(",",$var); 200 | my $rcvar=0; 201 | my $rc2var=0; 202 | foreach my $v (@vars) 203 | { 204 | $rcvar+=$rc{$v}; 205 | $rc2var+=$rc2{$v}; 206 | } 207 | 208 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 209 | #; 210 | 211 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 212 | 213 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 214 | { 215 | print OUT1 $ltr,"\n"; 216 | } 217 | } 218 | 219 | 220 | 221 | # called snv called by varscan and mutect, indel called varscan and strelka, 222 | if($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=varindel-pindel/) 223 | { 224 | $vaf_n=$temp[9]; 225 | $vaf_t=$temp[10]; 226 | @temp2=split(":",$vaf_n); 227 | #print $vaf_n,"\n"; 228 | my @ndp4=split(",",$temp2[3]); 229 | 230 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 231 | $ndp_ref=$ndp4[0]+$ndp4[1]; 232 | $ndp_var=$ndp4[2]+$ndp4[3]; 233 | #print $vaf_t,"\n"; 234 | @temp2=split(":",$vaf_t); 235 | my @tdp4=split(",",$temp2[3]); 236 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 237 | 238 | $tdp_ref=$tdp4[0]+$tdp4[1]; 239 | $tdp_var=$tdp4[2]+$tdp4[3]; 240 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 241 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 242 | { 243 | $ltr=~s/SVTYPE=//g; 244 | print OUT1 $ltr,"\n"; 245 | } 246 | } 247 | 248 | 249 | 250 | } 251 | } 252 | -------------------------------------------------------------------------------- /vaf_filter_v1.1.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | 5 | ### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ## 6 | 7 | ### add the filtering for indel length ## 8 | 9 | use strict; 10 | use warnings; 11 | die unless @ARGV == 1; 12 | my ($run_dir)=@ARGV; 13 | 14 | my $f_m=$run_dir."/merged.withmutect.vcf"; 15 | my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf"; 16 | my $f_vaf_out=$run_dir."/merged.withmutect.vaf"; 17 | my $min_vaf_somatic=0.05; 18 | my $min_vaf_pindel=0.1; 19 | my $max_vaf_germline=0.02; 20 | my $min_coverage=20; 21 | my $indel_max_size=100; 22 | 23 | open(OUT1,">$f_filter_out"); 24 | open(OUT2,">$f_vaf_out"); 25 | 26 | foreach my $l (`cat $f_m`) 27 | { 28 | my $ltr=$l; 29 | chomp($ltr); 30 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 31 | else { 32 | my @temp=split("\t",$ltr); 33 | #my $ref=$temp[3]; 34 | #my $var=$temp[4]; 35 | 36 | 37 | my $info=$temp[7]; 38 | my @temp2; 39 | my %rc; 40 | my %rc2; 41 | my $r_tot; 42 | my $r_tot2; 43 | my $vaf_n; 44 | my $vaf_t; 45 | my $ref; 46 | my $var; 47 | my $nt; 48 | my $ndp_ref; 49 | my $ndp_var; 50 | my $tdp_ref; 51 | my $tdp_var; 52 | 53 | $ref=$temp[3]; 54 | $var=$temp[4]; 55 | 56 | if(length($ref)>=$indel_max_size || length($var)>=$indel_max_size) { next; } 57 | 58 | #if($info=~/strelka-varscan/) 59 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/ || $info=~/set\=pindel-sindel/) 60 | { 61 | #print $info,"\n"; 62 | #; 63 | 64 | $vaf_n=$temp[11]; 65 | $vaf_t=$temp[12]; 66 | $ref=$temp[3]; 67 | $var=$temp[4]; 68 | $r_tot=0; 69 | 70 | @temp2=split(":",$vaf_n); 71 | %rc=(); 72 | #print $vaf_n,"\n"; 73 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 74 | #; 75 | #my @temp3=split(",",$temp2[0]); 76 | #$rc{'A'}=$temp3[0]; 77 | 78 | $rc{'A'}=(split(",",$temp2[0]))[0]; 79 | $rc{'C'}=(split(",",$temp2[1]))[0]; 80 | $rc{'G'}=(split(",",$temp2[4]))[0]; 81 | $rc{'T'}=(split(",",$temp2[7]))[0]; 82 | #print $vaf_n,"\n"; 83 | #print $vaf_t,"\n"; 84 | #; 85 | foreach my $nt (keys %rc) 86 | { 87 | $r_tot+=$rc{$nt}; 88 | #print $rc{$nt},"\n"; 89 | } 90 | 91 | @temp2=split(":",$vaf_t); 92 | 93 | %rc2=(); 94 | 95 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 96 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 97 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 98 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 99 | 100 | foreach $nt (sort keys %rc2) 101 | { 102 | $r_tot2+=$rc2{$nt}; 103 | #print $rc2{$nt},"\n"; 104 | } 105 | #print $ltr,"\n"; 106 | my @vars=split(",",$var); 107 | my $rcvar=0; 108 | my $rc2var=0; 109 | foreach my $v (@vars) 110 | { 111 | $rcvar+=$rc{$v}; 112 | $rc2var+=$rc2{$v}; 113 | } 114 | 115 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 116 | #; 117 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 118 | 119 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 120 | { 121 | print OUT1 $ltr,"\n"; 122 | } 123 | } 124 | 125 | elsif($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=pindel-varindel/ ) 126 | { 127 | $vaf_n=$temp[11]; 128 | $vaf_t=$temp[12]; 129 | @temp2=split(":",$vaf_n); 130 | #print $vaf_n,"\n"; 131 | my @ndp4=split(",",$temp2[3]); 132 | 133 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 134 | $ndp_ref=$ndp4[0]+$ndp4[1]; 135 | $ndp_var=$ndp4[2]+$ndp4[3]; 136 | #print $vaf_t,"\n"; 137 | @temp2=split(":",$vaf_t); 138 | my @tdp4=split(",",$temp2[3]); 139 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 140 | 141 | $tdp_ref=$tdp4[0]+$tdp4[1]; 142 | $tdp_var=$tdp4[2]+$tdp4[3]; 143 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 144 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 145 | { 146 | $ltr=~s/SVTYPE=//g; 147 | print OUT1 $ltr,"\n"; 148 | } 149 | } 150 | 151 | elsif($info=~/set\=pindel/) 152 | { 153 | 154 | $vaf_t=$temp[10]; 155 | $vaf_n=$temp[9]; 156 | if(!($vaf_t=~/\:/)) { next; } 157 | if(!($vaf_n=~/\:/)) { next; } 158 | 159 | @temp2=split(":",$vaf_n); 160 | my @ndp2=split(",",$temp2[1]); 161 | $ndp_ref=$ndp2[0]; 162 | $ndp_var=$ndp2[1]; 163 | @temp2=split(":",$vaf_t); 164 | my @tdp2=split(",",$temp2[1]); 165 | $tdp_ref=$tdp2[0]; 166 | $tdp_var=$tdp2[1]; 167 | #print $ndp_ref,"\t",$ndp_var,"\t",$tdp_ref,"\t",$tdp_var,"\n"; 168 | #; 169 | 170 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 171 | 172 | if($tdp_var/($tdp_var+$tdp_ref)>=$min_vaf_pindel && $ndp_var/($ndp_ref+$ndp_var)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 173 | { 174 | #print $ltr,"\n"; 175 | $ltr=~s/SVTYPE=//g; 176 | print OUT1 $ltr,"\n"; 177 | } 178 | 179 | } 180 | 181 | 182 | } 183 | } 184 | -------------------------------------------------------------------------------- /vaf_filter_v1.2.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | 5 | ### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ## 6 | 7 | ### add the filtering for indel length ## 8 | 9 | use strict; 10 | use warnings; 11 | die unless @ARGV == 1; 12 | my ($run_dir)=@ARGV; 13 | 14 | my $f_m=$run_dir."/merged.withmutect.vcf"; 15 | my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf"; 16 | my $f_vaf_out=$run_dir."/merged.withmutect.vaf"; 17 | my $min_vaf_somatic=0.05; 18 | my $min_vaf_pindel=0.1; 19 | my $max_vaf_germline=0.02; 20 | my $min_coverage=20; 21 | my $indel_max_size=100; 22 | 23 | open(OUT1,">$f_filter_out"); 24 | open(OUT2,">$f_vaf_out"); 25 | 26 | foreach my $l (`cat $f_m`) 27 | { 28 | my $ltr=$l; 29 | chomp($ltr); 30 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 31 | else { 32 | my @temp=split("\t",$ltr); 33 | #my $ref=$temp[3]; 34 | #my $var=$temp[4]; 35 | 36 | my $info=$temp[7]; 37 | my @temp2; 38 | my %rc; 39 | my %rc2; 40 | my $r_tot; 41 | my $r_tot2; 42 | my $vaf_n; 43 | my $vaf_t; 44 | my $ref; 45 | my $var; 46 | my $nt; 47 | my $ndp_ref; 48 | my $ndp_var; 49 | my $tdp_ref; 50 | my $tdp_var; 51 | 52 | $ref=$temp[3]; 53 | $var=$temp[4]; 54 | 55 | if(length($ref)>=$indel_max_size || length($var)>=$indel_max_size) { next; } 56 | 57 | #if($info=~/strelka-varscan/) and strelka-mutect ## 58 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/ ## 59 | if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 60 | # if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 61 | { 62 | 63 | #print $info,"\n"; 64 | #; 65 | #print $ltr,"\n"; 66 | 67 | $vaf_n=$temp[9]; 68 | $vaf_t=$temp[10]; 69 | $ref=$temp[3]; 70 | $var=$temp[4]; 71 | $r_tot=0; 72 | #print $ref,"\t",$var,"\n"; 73 | #print $vaf_n,"\n"; 74 | #print $vaf_t,"\n"; 75 | 76 | #; 77 | @temp2=split(":",$vaf_n); 78 | #%rc=(); 79 | #print $vaf_n,"\n"; 80 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 81 | #; 82 | #my @temp3=split(",",$temp2[0]); 83 | #$rc{'A'}=$temp3[0]; 84 | 85 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 86 | #...where: 87 | #ref_counts = value of FORMAT column value “TAR” 88 | #alt_counts = value of FORMAT column value “TIR” 89 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 90 | #alt_t1count = $alt_counts[0] (...likewise..) 91 | 92 | my $rcvar=(split(",",$temp2[-2]))[0]; 93 | my $rctot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 94 | my $rcref=$rctot-$rcvar; 95 | 96 | #$rc{'C'}=(split(",",$temp2[-2]))[0]; 97 | #print $vaf_n,"\n"; 98 | #print $vaf_t,"\n"; 99 | #; 100 | # foreach my $nt (keys %rc) 101 | # { 102 | # $r_tot+=$rc{$nt}; 103 | #print $rc{$nt},"\n"; 104 | # } 105 | 106 | @temp2=split(":",$vaf_t); 107 | 108 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 109 | #...where: 110 | #ref_counts = value of FORMAT column value “TAR” 111 | #alt_counts = value of FORMAT column value “TIR” 112 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 113 | #alt_t1count = $alt_counts[0] (...likewise..) 114 | 115 | my $rc2var=(split(",",$temp2[-2]))[0]; 116 | my $rc2tot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 117 | my $rc2ref=$rc2tot-$rc2var; 118 | 119 | #print $rcref,"\t",$rcvar,"\t",$rctot,"\n"; 120 | #print $rc2ref,"\t",$rc2var,"\t",$rc2tot,"\n"; 121 | #; 122 | 123 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 124 | #; 125 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rcref,"\t",$rcref/$rctot,"\t",$rcvar,"\t",$rcvar/$rctot,"\t",$rc2ref,"\t",$rc2ref/$rc2tot,"\t",$rc2var,"\t",$rc2var/$rc2tot,"\n"; 126 | 127 | if($rc2var/$rc2tot>=$min_vaf_somatic && $rcvar/$rctot<=$max_vaf_germline && $rc2tot>=$min_coverage && $rctot>=$min_coverage) 128 | { 129 | $ltr=~s/SVTYPE=//g; 130 | print OUT1 $ltr,"\n"; 131 | } 132 | } 133 | 134 | 135 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) for strelka 136 | 137 | #...where: 138 | 139 | #ref_counts = value of FORMAT column value “TAR” 140 | #alt_counts = value of FORMAT column value “TIR” 141 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 142 | #alt_t1count = $alt_counts[0] (...likewise..) 143 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 144 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 145 | { 146 | 147 | #print $info,"\n"; 148 | #; 149 | # print $ltr,"\n"; 150 | 151 | $vaf_n=$temp[9]; 152 | $vaf_t=$temp[10]; 153 | $ref=$temp[3]; 154 | $var=$temp[4]; 155 | $r_tot=0; 156 | # print $ref,"\t",$var,"\n"; 157 | # print $vaf_n,"\n"; 158 | # ; 159 | @temp2=split(":",$vaf_n); 160 | %rc=(); 161 | #print $vaf_n,"\n"; 162 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 163 | #; 164 | #my @temp3=split(",",$temp2[0]); 165 | #$rc{'A'}=$temp3[0]; 166 | 167 | $rc{'A'}=(split(",",$temp2[0]))[0]; 168 | $rc{'C'}=(split(",",$temp2[1]))[0]; 169 | $rc{'G'}=(split(",",$temp2[4]))[0]; 170 | $rc{'T'}=(split(",",$temp2[7]))[0]; 171 | #print $vaf_n,"\n"; 172 | #print $vaf_t,"\n"; 173 | #; 174 | foreach my $nt (keys %rc) 175 | { 176 | $r_tot+=$rc{$nt}; 177 | #print $rc{$nt},"\n"; 178 | } 179 | 180 | @temp2=split(":",$vaf_t); 181 | 182 | %rc2=(); 183 | 184 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 185 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 186 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 187 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 188 | 189 | foreach $nt (sort keys %rc2) 190 | { 191 | $r_tot2+=$rc2{$nt}; 192 | #print $rc2{$nt},"\n"; 193 | } 194 | #print $ltr,"\n"; 195 | my @vars=split(",",$var); 196 | my $rcvar=0; 197 | my $rc2var=0; 198 | foreach my $v (@vars) 199 | { 200 | $rcvar+=$rc{$v}; 201 | $rc2var+=$rc2{$v}; 202 | } 203 | 204 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 205 | #; 206 | 207 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 208 | 209 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage && $r_tot>=$min_coverage) 210 | { 211 | print OUT1 $ltr,"\n"; 212 | } 213 | } 214 | 215 | 216 | 217 | # called snv called by varscan and mutect, indel called varscan and strelka, 218 | if($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=varindel-pindel/) 219 | { 220 | $vaf_n=$temp[9]; 221 | $vaf_t=$temp[10]; 222 | @temp2=split(":",$vaf_n); 223 | #print $vaf_n,"\n"; 224 | my @ndp4=split(",",$temp2[3]); 225 | 226 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 227 | $ndp_ref=$ndp4[0]+$ndp4[1]; 228 | $ndp_var=$ndp4[2]+$ndp4[3]; 229 | #print $vaf_t,"\n"; 230 | @temp2=split(":",$vaf_t); 231 | my @tdp4=split(",",$temp2[3]); 232 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 233 | 234 | $tdp_ref=$tdp4[0]+$tdp4[1]; 235 | $tdp_var=$tdp4[2]+$tdp4[3]; 236 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 237 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage && $ndp_var+$ndp_ref>=$min_coverage) 238 | { 239 | $ltr=~s/SVTYPE=//g; 240 | print OUT1 $ltr,"\n"; 241 | } 242 | } 243 | 244 | 245 | 246 | } 247 | } 248 | -------------------------------------------------------------------------------- /vaf_filter_v1.3.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | 5 | ### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ## 6 | 7 | ### add the filtering for indel length ## 8 | 9 | use strict; 10 | use warnings; 11 | die unless @ARGV == 5; 12 | my ($run_dir,$min_vaf_somatic,$min_coverage_t,$min_coverage_n,$indel_max_size)=@ARGV; 13 | 14 | my $f_m=$run_dir."/merged.withmutect.vcf"; 15 | my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf"; 16 | my $f_vaf_out=$run_dir."/merged.withmutect.vaf"; 17 | #my $min_vaf_somatic=0.05; 18 | #my $min_vaf_pindel=0.1; 19 | my $max_vaf_germline=0.02; 20 | #my $min_coverage=20; 21 | #my $indel_max_size=100; 22 | 23 | open(OUT1,">$f_filter_out"); 24 | open(OUT2,">$f_vaf_out"); 25 | 26 | foreach my $l (`cat $f_m`) 27 | { 28 | my $ltr=$l; 29 | chomp($ltr); 30 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 31 | else { 32 | my @temp=split("\t",$ltr); 33 | #my $ref=$temp[3]; 34 | #my $var=$temp[4]; 35 | 36 | my $info=$temp[7]; 37 | my @temp2; 38 | my %rc; 39 | my %rc2; 40 | my $r_tot; 41 | my $r_tot2; 42 | my $vaf_n; 43 | my $vaf_t; 44 | my $ref; 45 | my $var; 46 | my $nt; 47 | my $ndp_ref; 48 | my $ndp_var; 49 | my $tdp_ref; 50 | my $tdp_var; 51 | 52 | $ref=$temp[3]; 53 | $var=$temp[4]; 54 | 55 | if(length($ref)>$indel_max_size || length($var)>$indel_max_size) { next; } 56 | 57 | #if($info=~/strelka-varscan/) and strelka-mutect ## 58 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/ ## 59 | if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 60 | # if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 61 | { 62 | 63 | #print $info,"\n"; 64 | #; 65 | #print $ltr,"\n"; 66 | 67 | $vaf_n=$temp[9]; 68 | $vaf_t=$temp[10]; 69 | $ref=$temp[3]; 70 | $var=$temp[4]; 71 | $r_tot=0; 72 | #print $ref,"\t",$var,"\n"; 73 | #print $vaf_n,"\n"; 74 | #print $vaf_t,"\n"; 75 | 76 | #; 77 | @temp2=split(":",$vaf_n); 78 | #%rc=(); 79 | #print $vaf_n,"\n"; 80 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 81 | #; 82 | #my @temp3=split(",",$temp2[0]); 83 | #$rc{'A'}=$temp3[0]; 84 | 85 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 86 | #...where: 87 | #ref_counts = value of FORMAT column value “TAR” 88 | #alt_counts = value of FORMAT column value “TIR” 89 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 90 | #alt_t1count = $alt_counts[0] (...likewise..) 91 | 92 | my $rcvar=(split(",",$temp2[-2]))[0]; 93 | my $rctot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 94 | my $rcref=$rctot-$rcvar; 95 | 96 | #$rc{'C'}=(split(",",$temp2[-2]))[0]; 97 | #print $vaf_n,"\n"; 98 | #print $vaf_t,"\n"; 99 | #; 100 | # foreach my $nt (keys %rc) 101 | # { 102 | # $r_tot+=$rc{$nt}; 103 | #print $rc{$nt},"\n"; 104 | # } 105 | 106 | @temp2=split(":",$vaf_t); 107 | 108 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 109 | #...where: 110 | #ref_counts = value of FORMAT column value “TAR” 111 | #alt_counts = value of FORMAT column value “TIR” 112 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 113 | #alt_t1count = $alt_counts[0] (...likewise..) 114 | 115 | my $rc2var=(split(",",$temp2[-2]))[0]; 116 | my $rc2tot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 117 | my $rc2ref=$rc2tot-$rc2var; 118 | 119 | #print $rcref,"\t",$rcvar,"\t",$rctot,"\n"; 120 | #print $rc2ref,"\t",$rc2var,"\t",$rc2tot,"\n"; 121 | #; 122 | 123 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 124 | #; 125 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rcref,"\t",$rcref/$rctot,"\t",$rcvar,"\t",$rcvar/$rctot,"\t",$rc2ref,"\t",$rc2ref/$rc2tot,"\t",$rc2var,"\t",$rc2var/$rc2tot,"\n"; 126 | 127 | if($rc2var/$rc2tot>=$min_vaf_somatic && $rcvar/$rctot<=$max_vaf_germline && $rc2tot>=$min_coverage_t && $rctot>=$min_coverage_n) 128 | { 129 | $ltr=~s/SVTYPE=//g; 130 | print OUT1 $ltr,"\n"; 131 | } 132 | } 133 | 134 | 135 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) for strelka 136 | 137 | #...where: 138 | 139 | #ref_counts = value of FORMAT column value “TAR” 140 | #alt_counts = value of FORMAT column value “TIR” 141 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 142 | #alt_t1count = $alt_counts[0] (...likewise..) 143 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 144 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 145 | { 146 | 147 | #print $info,"\n"; 148 | #; 149 | # print $ltr,"\n"; 150 | 151 | $vaf_n=$temp[9]; 152 | $vaf_t=$temp[10]; 153 | $ref=$temp[3]; 154 | $var=$temp[4]; 155 | $r_tot=0; 156 | # print $ref,"\t",$var,"\n"; 157 | # print $vaf_n,"\n"; 158 | # ; 159 | @temp2=split(":",$vaf_n); 160 | %rc=(); 161 | #print $vaf_n,"\n"; 162 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 163 | #; 164 | #my @temp3=split(",",$temp2[0]); 165 | #$rc{'A'}=$temp3[0]; 166 | 167 | $rc{'A'}=(split(",",$temp2[0]))[0]; 168 | $rc{'C'}=(split(",",$temp2[1]))[0]; 169 | $rc{'G'}=(split(",",$temp2[4]))[0]; 170 | $rc{'T'}=(split(",",$temp2[7]))[0]; 171 | #$rc{'A'}=(split(",",$temp2[2]))[0]; 172 | #$rc{'C'}=(split(",",$temp2[3]))[0]; 173 | #$rc{'G'}=(split(",",$temp2[6]))[0]; 174 | #$rc{'T'}=(split(",",$temp2[9]))[0]; 175 | #print $vaf_n,"\n"; 176 | #print $vaf_t,"\n"; 177 | #; 178 | foreach my $nt (keys %rc) 179 | { 180 | $r_tot+=$rc{$nt}; 181 | #print $rc{$nt},"\n"; 182 | } 183 | 184 | @temp2=split(":",$vaf_t); 185 | 186 | %rc2=(); 187 | 188 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 189 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 190 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 191 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 192 | 193 | #$rc2{'A'}=(split(",",$temp2[2]))[0]; 194 | #$rc2{'C'}=(split(",",$temp2[3]))[0]; 195 | #$rc2{'G'}=(split(",",$temp2[6]))[0]; 196 | #$rc2{'T'}=(split(",",$temp2[9]))[0]; 197 | 198 | foreach $nt (sort keys %rc2) 199 | { 200 | $r_tot2+=$rc2{$nt}; 201 | #print $rc2{$nt},"\n"; 202 | } 203 | #print $ltr,"\n"; 204 | my @vars=split(",",$var); 205 | my $rcvar=0; 206 | my $rc2var=0; 207 | foreach my $v (@vars) 208 | { 209 | $rcvar+=$rc{$v}; 210 | $rc2var+=$rc2{$v}; 211 | } 212 | 213 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 214 | #; 215 | 216 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 217 | 218 | if($rc2var/$r_tot2>=$min_vaf_somatic && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage_t && $r_tot>=$min_coverage_n) 219 | { 220 | print OUT1 $ltr,"\n"; 221 | } 222 | } 223 | 224 | 225 | 226 | # called snv called by varscan and mutect, indel called varscan and strelka, 227 | if($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=varindel-pindel/) 228 | { 229 | $vaf_n=$temp[9]; 230 | $vaf_t=$temp[10]; 231 | @temp2=split(":",$vaf_n); 232 | #print $vaf_n,"\n"; 233 | my @ndp4=split(",",$temp2[3]); 234 | 235 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 236 | $ndp_ref=$ndp4[0]+$ndp4[1]; 237 | $ndp_var=$ndp4[2]+$ndp4[3]; 238 | #print $vaf_t,"\n"; 239 | @temp2=split(":",$vaf_t); 240 | my @tdp4=split(",",$temp2[3]); 241 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 242 | 243 | $tdp_ref=$tdp4[0]+$tdp4[1]; 244 | $tdp_var=$tdp4[2]+$tdp4[3]; 245 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 246 | if($tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage_t && $ndp_var+$ndp_ref>=$min_coverage_n) 247 | { 248 | $ltr=~s/SVTYPE=//g; 249 | print OUT1 $ltr,"\n"; 250 | } 251 | } 252 | 253 | 254 | 255 | } 256 | } 257 | -------------------------------------------------------------------------------- /vaf_filter_v1.4.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl 2 | 3 | ## tumor >= 5% and normal <=1% 4 | 5 | ### pindel tumor >=10% since the vaf calculation underestimate the ref coverage ## 6 | 7 | ### add the filtering for indel length ## 8 | 9 | ## remove tumor >= 5% cut-off for smg list, Apr 23, 2020 ## 10 | 11 | use strict; 12 | use warnings; 13 | die unless @ARGV == 7; 14 | 15 | my ($run_dir,$sn,$min_vaf_somatic,$min_coverage_t,$min_coverage_n,$indel_max_size,$f_smg_list)=@ARGV; 16 | 17 | my $f_m=$run_dir."/merged.withmutect.vcf"; 18 | my $f_maf=$run_dir."/".$sn.".withmutect.maf"; 19 | my $f_filter_out=$run_dir."/merged.filtered.withmutect.vcf"; 20 | my $f_vaf_out=$run_dir."/merged.withmutect.vaf"; 21 | 22 | #my $min_vaf_somatic=0.05; 23 | #my $min_vaf_pindel=0.1; 24 | my $max_vaf_germline=0.02; 25 | #my $min_coverage=20; 26 | #my $indel_max_size=100; 27 | my %smg=(); 28 | my %m2g=(); 29 | 30 | 31 | open(OUT1,">$f_filter_out"); 32 | open(OUT2,">$f_vaf_out"); 33 | 34 | if($f_smg_list ne "" && (-e $f_smg_list)) 35 | { 36 | foreach my $l (`cat $f_smg_list`) 37 | { 38 | my $ltr=$l; 39 | chomp($ltr); 40 | $smg{$ltr}=1; 41 | } 42 | } 43 | 44 | ## generate mutation to gene name table ## 45 | 46 | foreach my $l (`cat $f_maf`) 47 | { 48 | my $ltr=$l; 49 | chomp($ltr); 50 | if($ltr=~/^Hugo/) { next; } 51 | my @t=split("\t",$ltr); 52 | if(defined $smg{$t[0]}) 53 | { 54 | #print $t[0],"\t",$t[4],"\t",$t[5],"\n"; ; 55 | $m2g{$t[4]}{$t[5]}=$t[0]; 56 | } 57 | } 58 | 59 | foreach my $l (`cat $f_m`) 60 | { 61 | my $ltr=$l; 62 | chomp($ltr); 63 | if($ltr=~/^#/) { print OUT1 $ltr,"\n"; next; } 64 | else { 65 | my @temp=split("\t",$ltr); 66 | #my $ref=$temp[3]; 67 | #my $var=$temp[4]; 68 | 69 | my $info=$temp[7]; 70 | my @temp2; 71 | my %rc; 72 | my %rc2; 73 | my $r_tot; 74 | my $r_tot2; 75 | my $vaf_n; 76 | my $vaf_t; 77 | my $ref; 78 | my $var; 79 | my $nt; 80 | my $ndp_ref; 81 | my $ndp_var; 82 | my $tdp_ref; 83 | my $tdp_var; 84 | my $chr=$temp[0]; 85 | my $p=$temp[1]; 86 | 87 | $ref=$temp[3]; 88 | $var=$temp[4]; 89 | 90 | if(length($ref)>$indel_max_size || length($var)>$indel_max_size) { next; } 91 | 92 | #if($info=~/strelka-varscan/) and strelka-mutect ## 93 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/ ## 94 | if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 95 | # if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 96 | { 97 | 98 | #print $info,"\n"; 99 | #; 100 | #print $ltr,"\n"; 101 | 102 | $vaf_n=$temp[9]; 103 | $vaf_t=$temp[10]; 104 | $ref=$temp[3]; 105 | $var=$temp[4]; 106 | $r_tot=0; 107 | #print $ref,"\t",$var,"\n"; 108 | #print $vaf_n,"\n"; 109 | #print $vaf_t,"\n"; 110 | 111 | #; 112 | @temp2=split(":",$vaf_n); 113 | #%rc=(); 114 | #print $vaf_n,"\n"; 115 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 116 | #; 117 | #my @temp3=split(",",$temp2[0]); 118 | #$rc{'A'}=$temp3[0]; 119 | 120 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 121 | #...where: 122 | #ref_counts = value of FORMAT column value “TAR” 123 | #alt_counts = value of FORMAT column value “TIR” 124 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 125 | #alt_t1count = $alt_counts[0] (...likewise..) 126 | 127 | my $rcvar=(split(",",$temp2[-2]))[0]; 128 | my $rctot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 129 | my $rcref=$rctot-$rcvar; 130 | 131 | #$rc{'C'}=(split(",",$temp2[-2]))[0]; 132 | #print $vaf_n,"\n"; 133 | #print $vaf_t,"\n"; 134 | #; 135 | # foreach my $nt (keys %rc) 136 | # { 137 | # $r_tot+=$rc{$nt}; 138 | #print $rc{$nt},"\n"; 139 | # } 140 | 141 | @temp2=split(":",$vaf_t); 142 | 143 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) 144 | #...where: 145 | #ref_counts = value of FORMAT column value “TAR” 146 | #alt_counts = value of FORMAT column value “TIR” 147 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 148 | #alt_t1count = $alt_counts[0] (...likewise..) 149 | 150 | my $rc2var=(split(",",$temp2[-2]))[0]; 151 | my $rc2tot=(split(",",$temp2[-3]))[0]+(split(",",$temp2[-2]))[0]; 152 | my $rc2ref=$rc2tot-$rc2var; 153 | 154 | #print $rcref,"\t",$rcvar,"\t",$rctot,"\n"; 155 | #print $rc2ref,"\t",$rc2var,"\t",$rc2tot,"\n"; 156 | #; 157 | 158 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 159 | #; 160 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rcref,"\t",$rcref/$rctot,"\t",$rcvar,"\t",$rcvar/$rctot,"\t",$rc2ref,"\t",$rc2ref/$rc2tot,"\t",$rc2var,"\t",$rc2var/$rc2tot,"\n"; 161 | 162 | if((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $rc2var/$rc2tot>=$min_vaf_somatic) && $rcvar/$rctot<=$max_vaf_germline && $rc2tot>=$min_coverage_t && $rctot>=$min_coverage_n) 163 | { 164 | $ltr=~s/SVTYPE=//g; 165 | print OUT1 $ltr,"\n"; 166 | } 167 | } 168 | 169 | 170 | #Somatic indel indel allele frequency is: alt_t1count / (ref_t1count + alt_t1count) for strelka 171 | 172 | #...where: 173 | 174 | #ref_counts = value of FORMAT column value “TAR” 175 | #alt_counts = value of FORMAT column value “TIR” 176 | #ref_t1count = $ref_counts[0] (use the tier1 counts -- the first value in the comma-delimited list) 177 | #alt_t1count = $alt_counts[0] (...likewise..) 178 | if($info=~/set\=strelka-varscan/ || $info=~/set\=strelka-mutect/) 179 | #if($info=~/set\=sindel-varindel/ || $info=~/set\=sindel-pindel/) 180 | { 181 | 182 | #print $info,"\n"; 183 | #; 184 | # print $ltr,"\n"; 185 | 186 | $vaf_n=$temp[9]; 187 | $vaf_t=$temp[10]; 188 | $ref=$temp[3]; 189 | $var=$temp[4]; 190 | $r_tot=0; 191 | # print $ref,"\t",$var,"\n"; 192 | # print $vaf_n,"\n"; 193 | # ; 194 | @temp2=split(":",$vaf_n); 195 | %rc=(); 196 | #print $vaf_n,"\n"; 197 | #print $temp2[0],"\t",$temp2[1],"\t",$temp2[4],"\t",$temp2[7],"\n"; 198 | #; 199 | #my @temp3=split(",",$temp2[0]); 200 | #$rc{'A'}=$temp3[0]; 201 | 202 | $rc{'A'}=(split(",",$temp2[0]))[0]; 203 | $rc{'C'}=(split(",",$temp2[1]))[0]; 204 | $rc{'G'}=(split(",",$temp2[4]))[0]; 205 | $rc{'T'}=(split(",",$temp2[7]))[0]; 206 | #$rc{'A'}=(split(",",$temp2[2]))[0]; 207 | #$rc{'C'}=(split(",",$temp2[3]))[0]; 208 | #$rc{'G'}=(split(",",$temp2[6]))[0]; 209 | #$rc{'T'}=(split(",",$temp2[9]))[0]; 210 | #print $vaf_n,"\n"; 211 | #print $vaf_t,"\n"; 212 | #; 213 | foreach my $nt (keys %rc) 214 | { 215 | $r_tot+=$rc{$nt}; 216 | #print $rc{$nt},"\n"; 217 | } 218 | 219 | @temp2=split(":",$vaf_t); 220 | 221 | %rc2=(); 222 | 223 | $rc2{'A'}=(split(",",$temp2[0]))[0]; 224 | $rc2{'C'}=(split(",",$temp2[1]))[0]; 225 | $rc2{'G'}=(split(",",$temp2[4]))[0]; 226 | $rc2{'T'}=(split(",",$temp2[7]))[0]; 227 | 228 | #$rc2{'A'}=(split(",",$temp2[2]))[0]; 229 | #$rc2{'C'}=(split(",",$temp2[3]))[0]; 230 | #$rc2{'G'}=(split(",",$temp2[6]))[0]; 231 | #$rc2{'T'}=(split(",",$temp2[9]))[0]; 232 | 233 | foreach $nt (sort keys %rc2) 234 | { 235 | $r_tot2+=$rc2{$nt}; 236 | #print $rc2{$nt},"\n"; 237 | } 238 | #print $ltr,"\n"; 239 | my @vars=split(",",$var); 240 | my $rcvar=0; 241 | my $rc2var=0; 242 | foreach my $v (@vars) 243 | { 244 | $rcvar+=$rc{$v}; 245 | $rc2var+=$rc2{$v}; 246 | } 247 | 248 | #print $rc{$ref},"\t",$rcvar,"\t",$rc2{$ref},"\t",$rc2var,"\n"; 249 | #; 250 | 251 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$rc{$ref},"\t",$rc{$ref}/$r_tot,"\t",$rcvar,"\t",$rcvar/$r_tot,"\t",$rc2{$ref},"\t",$rc2{$ref}/$r_tot2,"\t",$rc2var,"\t",$rc2var/$r_tot2,"\n"; 252 | 253 | if((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $rc2var/$r_tot2>=$min_vaf_somatic) && $rcvar/$r_tot<=$max_vaf_germline && $r_tot2>=$min_coverage_t && $r_tot>=$min_coverage_n) 254 | { 255 | print OUT1 $ltr,"\n"; 256 | } 257 | } 258 | 259 | 260 | 261 | # called snv called by varscan and mutect, indel called varscan and strelka, 262 | if($info=~/set\=varscan-mutect/ || $info=~/set\=varindel-sindel/ || $info=~/set\=varindel-pindel/) 263 | { 264 | $vaf_n=$temp[9]; 265 | $vaf_t=$temp[10]; 266 | @temp2=split(":",$vaf_n); 267 | #print $vaf_n,"\n"; 268 | my @ndp4=split(",",$temp2[3]); 269 | 270 | if(scalar @ndp4<4) { @ndp4=split(",",$temp2[2]); } 271 | $ndp_ref=$ndp4[0]+$ndp4[1]; 272 | $ndp_var=$ndp4[2]+$ndp4[3]; 273 | #print $vaf_t,"\n"; 274 | @temp2=split(":",$vaf_t); 275 | my @tdp4=split(",",$temp2[3]); 276 | if(scalar @tdp4<4) { @tdp4=split(",",$temp2[2]); } 277 | 278 | $tdp_ref=$tdp4[0]+$tdp4[1]; 279 | $tdp_var=$tdp4[2]+$tdp4[3]; 280 | print OUT2 $temp[0],"\t",$temp[1],"\t",$temp[2],"\t",$temp[3],"\t",$temp[4],"\t",$info,"\t",$ndp_ref,"\t",$ndp_ref/($ndp_ref+$ndp_var),"\t",$ndp_var,"\t",$ndp_var/($ndp_var+$ndp_ref),"\t",$tdp_ref,"\t",$tdp_ref/($tdp_ref+$tdp_var),"\t",$tdp_var,"\t",$tdp_var/($tdp_var+$tdp_ref),"\n"; 281 | if((defined $m2g{$chr}{$p} || $m2g{$chr}{$p-1} || $m2g{$chr}{$p+1} || $tdp_var/($tdp_var+$tdp_ref) >=$min_vaf_somatic) && $ndp_var/($ndp_var+$ndp_ref)<=$max_vaf_germline && $tdp_var+$tdp_ref>=$min_coverage_t && $ndp_var+$ndp_ref>=$min_coverage_n) 282 | { 283 | $ltr=~s/SVTYPE=//g; 284 | print OUT1 $ltr,"\n"; 285 | } 286 | } 287 | 288 | 289 | 290 | } 291 | } 292 | -------------------------------------------------------------------------------- /vep_annotator.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | #---------------------------------- 3 | # @name GenomeVIP VEP annotator script 4 | # @author R. Jay Mashl 5 | # @version 0.2: allow VEP options to be passed 6 | # @version 0.1: original version 7 | #-------------------------------------- 8 | ## song changed the parameter for vep 9 | ### 12/13/17 ### 10 | use strict; 11 | use warnings; 12 | 13 | use Cwd; 14 | use Carp; 15 | use FileHandle; 16 | use IO::File; 17 | use Getopt::Long; 18 | use POSIX qw( WIFEXITED ); 19 | use File::Temp qw/ tempfile /; 20 | 21 | # get paras from config file 22 | my (%paras); 23 | map {chomp; if(!/^[#;]/ && /=/) { @_ = split /=/; $_[1] =~ s/^\s+//; $_[1] =~ s/\s+$//; my $v = $_[1]; print $v."\n"; $_[0] =~ s/ //g; $paras{ (split /\./, $_[0])[-1] } = $v } } (<>); 24 | map { print; print "\t"; print $paras{$_}; print "\n" } keys %paras; 25 | 26 | # check if options are present 27 | my $opts=""; 28 | if( exists($paras{'vep_opts'}) ) { $opts = $paras{'vep_opts'} }; 29 | 30 | my $cmd=""; 31 | 32 | # split off original header 33 | my (undef, $tmp_orig_calls) = tempfile(); 34 | $cmd="/bin/grep -v ^# $paras{'vcf'} > $tmp_orig_calls"; 35 | system($cmd); 36 | 37 | # run vep 38 | my (undef, $tmp_vep_out) = tempfile(); 39 | 40 | ### wxs less mutation ## 41 | #$cmd = "perl $paras{'vep_cmd'} --offline --cache --dir $paras{'cachedir'} --polyphen b --gmaf --maf_1kg --maf_esp --assembly $paras{'assembly'} --fork 4 --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --vcf -i $tmp_orig_calls -o $tmp_vep_out --force_overwrite --fasta $paras{'reffasta'}"; 42 | 43 | #$cmd = "perl $paras{'vep_cmd'} --offline --cache --dir $paras{'cachedir'} --polyphen b --gmaf --maf_1kg --maf_esp --assembly $paras{'assembly'} --fork 4 --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --input_file $paras{'vcf'} --output_file $paras{'output'} --force_overwrite --fasta $paras{'reffasta'}"; 44 | 45 | $cmd = "/usr/bin/perl $paras{'vep_cmd'} $opts --buffer_size 300 --offline --cache --dir $paras{'cachedir'} --assembly $paras{'assembly'} --fork 8 --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --tsl --no_check_variants_order --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --vcf -i $tmp_orig_calls -o $tmp_vep_out --force_overwrite --fasta $paras{'reffasta'}"; 46 | 47 | ## for wgs simple ## 48 | 49 | #$cmd = "perl $paras{'vep_cmd'} $opts --buffer_size 10000 --offline --cache --dir $paras{'cachedir'} --assembly $paras{'assembly'} --fork 4 --format vcf --vcf -i $tmp_orig_calls -o $tmp_vep_out --force_overwrite --fasta $paras{'reffasta'}"; 50 | 51 | #$cmd = "perl $paras{'vep_cmd'} $opts --buffer_size 1000 --offline --cache --dir $paras{'cachedir'} --assembly $paras{'assembly'} --fork 4 --format vcf --vcf -i $tmp_orig_calls -o $tmp_vep_out --force_overwrite --everything --fasta $paras{'reffasta'}"; 52 | 53 | #variant_effect_predictor.pl --species $species --assembly $ncbi_build --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta $ref_fasta --format vcf --input_file $input_vcf --output_file $output_vcf 54 | 55 | system($cmd); 56 | 57 | # re-merge headers and move 58 | my (undef, $tmp_merge) = tempfile(); 59 | $cmd = "grep ^##fileformat $tmp_vep_out > $tmp_merge"; 60 | system($cmd); 61 | 62 | $cmd = "grep ^# $paras{'vcf'} | grep -v ^##fileformat | grep -v ^#CHROM >> $tmp_merge"; 63 | system($cmd); 64 | $cmd = "grep -v ^##fileformat $tmp_vep_out >> $tmp_merge"; 65 | system($cmd); 66 | $cmd = "cat $tmp_merge > $paras{'output'}"; 67 | system($cmd); 68 | 69 | #Save other output 70 | my @suffix=("_summary.html", "_warnings.txt"); 71 | foreach (@suffix) { 72 | my $file = $tmp_vep_out.$_; if ( -e $file ) { $cmd = "cat $file > $paras{'output'}".$_; system($cmd); } 73 | } 74 | # clean up 75 | $cmd = "rm -f $tmp_orig_calls $tmp_vep_out"."*"." ".$tmp_merge; 76 | system($cmd); 77 | 78 | 1; 79 | 80 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b10: -------------------------------------------------------------------------------- 1 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 1 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 8 | 9 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 10 | 11 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 6 12 | 13 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 14 | 15 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 16 | 17 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 18 | 19 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 20 | 21 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b10 --log /gscmnt/gc2541/scao/alchemist/somatic/b10.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 14 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b11: -------------------------------------------------------------------------------- 1 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 1 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 8 | 9 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 10 | 11 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 6 12 | 13 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 14 | 15 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 16 | 17 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 18 | 19 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 20 | 21 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b11 --log /gscmnt/gc2541/scao/alchemist/somatic/b11.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 14 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b12: -------------------------------------------------------------------------------- 1 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 1 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 8 | 9 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 10 | 11 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 6 12 | 13 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 14 | 15 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 16 | 17 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 18 | 19 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 20 | 21 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 22 | 23 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 24 | 25 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b12 --log /gscmnt/gc2541/scao/alchemist/somatic/b12.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 14 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b2: -------------------------------------------------------------------------------- 1 | 2 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 1 3 | 4 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 2 5 | 6 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 3 7 | 8 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 4 9 | 10 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 5 11 | 12 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 6 13 | 14 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 7 15 | 16 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 8 17 | 18 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 9 19 | 20 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 10 21 | 22 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 11 23 | 24 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 12 25 | 26 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 13 27 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b4: -------------------------------------------------------------------------------- 1 | ## b1 batch ## 2 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 1 3 | 4 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 5 | 6 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 7 | 8 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 9 | 10 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 11 | 12 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 6 13 | 14 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 15 | 16 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 17 | 18 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 19 | 20 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 21 | 22 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 23 | 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b4 --log /gscmnt/gc2541/scao/alchemist/somatic/b4.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 28 | 29 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b6: -------------------------------------------------------------------------------- 1 | ## b1 batch ## 2 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 1 3 | 4 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 2 5 | 6 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 3 7 | 8 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 4 9 | 10 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 11 | 12 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 6 13 | 14 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 15 | 16 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 17 | 18 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 19 | 20 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 21 | 22 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 23 | 24 | 25 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 26 | 27 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 28 | 29 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b6 --log /gscmnt/gc2541/scao/alchemist/somatic/b6.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 14 30 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b8: -------------------------------------------------------------------------------- 1 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 1 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 2 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 3 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 4 8 | 9 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 5 10 | 11 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --sre 1 --step 6 12 | 13 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 7 14 | 15 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 8 16 | 17 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 9 18 | 19 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 10 20 | 21 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 11 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 12 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 13 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/alchemist/somatic/b8 --log /gscmnt/gc2541/scao/alchemist/somatic/b8.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/cancer_gene_list_cell_uniq.tsv --step 14 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_b9: -------------------------------------------------------------------------------- 1 | 2 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 1 3 | 4 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 2 --sre 1 5 | 6 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 3 7 | 8 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 4 --sre 1 9 | 10 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 5 11 | 12 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 6 13 | 14 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 7 15 | 16 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 8 17 | 18 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 9 19 | 20 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 10 21 | 22 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 11 23 | 24 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 12 25 | 26 | #perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9 --log /storage1/fs1/songcao/Active/Project/GDAN/Alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 13 27 | -------------------------------------------------------------------------------- /work_log_run_alchemist_unfinished: -------------------------------------------------------------------------------- 1 | 2 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 1 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 3 | 4 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 2 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 5 | 6 | 7 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 3 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 8 | 9 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 4 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 10 | 11 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 5 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 12 | 13 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 6 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 14 | 15 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 7 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 16 | 17 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 8 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 18 | 19 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 9 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 20 | 21 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 10 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 22 | 23 | #perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 11 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 24 | 25 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 12 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 26 | 27 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --step 13 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_unfinished2: -------------------------------------------------------------------------------- 1 | 2 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 1 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 3 | 4 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 2 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 5 | 6 | 7 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 3 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 8 | 9 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 4 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 10 | 11 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 5 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 12 | 13 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 6 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 14 | 15 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 7 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 16 | 17 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 8 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 18 | 19 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 9 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 20 | 21 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 10 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 22 | 23 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 11 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 24 | 25 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 12 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 26 | 27 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 13 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 28 | -------------------------------------------------------------------------------- /work_log_run_alchemist_unfinished3: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 1 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 2 | 3 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 2 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 4 | 5 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 3 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 6 | 7 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 4 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 8 | 9 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 5 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 10 | 11 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 6 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 12 | 13 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 7 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 14 | 15 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 8 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 16 | 17 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 9 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 18 | 19 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 10 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 20 | 21 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 11 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 22 | 23 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 12 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 24 | 25 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/unfinished3.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 13 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 26 | -------------------------------------------------------------------------------- /work_log_run_confirmatory_gbm_b1: -------------------------------------------------------------------------------- 1 | ## b1 batch ## 2 | mkdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log 3 | 4 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1 5 | 6 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2 7 | 8 | 9 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3 10 | 11 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4 12 | 13 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5 14 | 15 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6 16 | 17 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7 18 | 19 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8 20 | 21 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12 28 | 29 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13 30 | 31 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b1/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 14 32 | 33 | ## b2 batch 34 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1 35 | 36 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2 37 | 38 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3 39 | 40 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4 41 | 42 | 43 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5 44 | 45 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6 46 | 47 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7 48 | 49 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8 50 | 51 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9 52 | 53 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10 54 | 55 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11 56 | 57 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12 58 | 59 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic --log /gscmnt/gc2521/dinglab/scao/cptac3/GBM/confirmatory/exome.hg38/b2/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13 60 | -------------------------------------------------------------------------------- /work_log_run_confirmatory_gbm_realign.b1: -------------------------------------------------------------------------------- 1 | ## b1 batch ## 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3 8 | 9 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4 10 | 11 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5 12 | 13 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6 14 | 15 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7 16 | 17 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8 18 | 19 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9 20 | 21 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b1 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b1.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 13 28 | -------------------------------------------------------------------------------- /work_log_run_confirmatory_gbm_realign.b2: -------------------------------------------------------------------------------- 1 | ## b2 batch ## 2 | 3 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 1 4 | 5 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 2 6 | 7 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 3 8 | 9 | #perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 4 10 | 11 | 12 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 5 13 | 14 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 6 15 | 16 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 7 17 | 18 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 8 19 | 20 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 9 21 | 22 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 10 23 | 24 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 11 25 | 26 | perl somaticwrapper.pl --rdir /gscmnt/gc2541/scao/gbm2/somatic/realign.b2 --log /gscmnt/gc2541/scao/gbm2/somatic/realign.b2.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv --step 12 27 | -------------------------------------------------------------------------------- /work_log_run_ctspkirc: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 1 2 | 3 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 2 4 | 5 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 3 6 | 7 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 4 8 | 9 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 5 10 | 11 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 6 --sre 1 12 | 13 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 7 14 | 15 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 8 16 | 17 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --step 9 18 | 19 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10 20 | 21 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11 22 | 23 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12 24 | 25 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 26 | 27 | 28 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 3 29 | 30 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 3 31 | 32 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 8 33 | 34 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 9 35 | 36 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10 37 | 38 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11 39 | 40 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12 41 | 42 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2 --log /scratch1/fs1/dinglab/scao/sw/ctspkirc.unfinished2.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 43 | 44 | 45 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 8 46 | 47 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 5 48 | 49 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 7 50 | 51 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 9 52 | 53 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 10 54 | 55 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 11 56 | 57 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/unfinished.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12 58 | 59 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/ctspkirc --log /storage1/fs1/dinglab/Active/Projects/scao/ctspkirc/sw/b1/ctspkirc.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.bailey.cell.kirc.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 60 | -------------------------------------------------------------------------------- /work_log_run_dlbcl: -------------------------------------------------------------------------------- 1 | mkdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log 2 | 3 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 1 4 | 5 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 2 6 | 7 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 3 8 | 9 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 4 10 | 11 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 5 12 | 13 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 6 14 | 15 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 7 16 | 17 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 8 18 | 19 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 9 20 | 21 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 10 22 | 23 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 11 24 | 25 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 12 26 | 27 | perl somaticwrapper.pl --rdir /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic --log /gscmnt/gc2517/dinglab/gdan/dlbcl/somatic.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.bailey.cell.dlbc.tsv --step 13 28 | -------------------------------------------------------------------------------- /work_log_run_gbm: -------------------------------------------------------------------------------- 1 | 2 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/cptac3/GBM/rescue.ATRX --log /gscmnt/gc2521/dinglab/cptac3/GBM/somatic.rec.smg.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --step 5 3 | 4 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/cptac3/GBM/rescue.ATRX --log /gscmnt/gc2521/dinglab/cptac3/GBM/somatic.rec.smg.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --step 10 5 | 6 | ## run step 11 with smg option ## 7 | 8 | 9 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/cptac3/GBM/rescue.ATRX --log /gscmnt/gc2521/dinglab/cptac3/GBM/somatic.rec.smg.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --step 11 --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv 10 | 11 | 12 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/cptac3/GBM/rescue.ATRX --log /gscmnt/gc2521/dinglab/cptac3/GBM/somatic.rec.smg.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --step 12 --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv 13 | 14 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/cptac3/GBM/rescue.ATRX --log /gscmnt/gc2521/dinglab/cptac3/GBM/somatic.rec.smg.log --ref /gscmnt/gc2521/dinglab/mwyczalk/somatic-wrapper-data/image.data/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q research-hpc --step 13 --smg /gscmnt/gc3027/dinglab/medseq/smg_database/smg.gbm.tsv 15 | 16 | -------------------------------------------------------------------------------- /work_log_run_htan_brca: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /gscmnt/gc2521/dinglab/austins2/htan_breast/SW/input2 --log /gscmnt/gc2521/dinglab/austins2/htan_breast/SW/log --ref /gscmnt/gc7202/dinglab/common/Reference/A_Reference/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --smg /gscmnt/gc2521/dinglab/austins2/tools/SMG/smg_Bailey_BRCA.tsv --q research-hpc --step 1 2 | 3 | 4 | 5 | -------------------------------------------------------------------------------- /work_log_run_mild: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 1 2 | 3 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 2 4 | 5 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 3 6 | 7 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 4 8 | 9 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 5 10 | 11 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 6 12 | 13 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 7 14 | 15 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 8 --sre 1 16 | 17 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 9 --sre 1 18 | 19 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 10 --sre 1 20 | 21 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 11 --sre 1 22 | 23 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1 24 | 25 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mild --log /scratch1/fs1/dinglab/scao/sw/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1 26 | 27 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1 28 | 29 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mild.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 13 --sre 1 30 | -------------------------------------------------------------------------------- /work_log_run_mild_v102: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 11 --sre 1 2 | 3 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1 4 | 5 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1 6 | 7 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102 --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 12 --sre 1 8 | 9 | perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102 --log /storage1/fs1/dinglab/Active/Projects/scao/mild/datafreeze/somatic.WXS/mildvep102.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q dinglab --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1 10 | -------------------------------------------------------------------------------- /work_log_run_mild_wgs: -------------------------------------------------------------------------------- 1 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 1 2 | 3 | 4 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 2 5 | 6 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 3 7 | 8 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 4 9 | 10 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 5 11 | 12 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 6 13 | 14 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 7 15 | 16 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 8 17 | 18 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 9 19 | 20 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 10 21 | 22 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 11 23 | 24 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgstest --log /scratch1/fs1/dinglab/scao/sw/mildwgstest.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 11 --sre 1 25 | 26 | perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildwgs --log /scratch1/fs1/dinglab/scao/sw/mildwgs.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --wgs 1 --step 11 --sre 1 27 | -------------------------------------------------------------------------------- /work_log_run_test: -------------------------------------------------------------------------------- 1 | # perl somaticwrapper.pl --rdir /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9 --log /storage1/fs1/dinglab/Active/Projects/scao/alchemist/somatic/b9.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv --users songcao --groupname SomaticWXS --step 4 --sre 1 2 | 3 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 1 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 4 | 5 | 6 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 2 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 7 | 8 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 3 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 9 | 10 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 4 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 11 | 12 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 5 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 13 | 14 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 6 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 15 | 16 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 7 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 17 | 18 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 8 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 19 | 20 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 9 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 21 | 22 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 10 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 23 | 24 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 11 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 25 | 26 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 12 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 27 | 28 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 13 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 29 | 30 | perl somaticwrapper.pl --rdir /storage1/fs1/songcao/Active/Project/CPTAC/somatic --log /storage1/fs1/songcao/Active/Project/CPTAC/somatic.log --ref /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --step 14 --smg /storage1/fs1/songcao/Active/Database/smg_database/cancer_gene_list_cell_uniq.tsv -users songcao --groupname SomaticWXS --sre 1 31 | --------------------------------------------------------------------------------