├── 1KG ├── 1kg_ny_download_100_genotypes.sh ├── 1kg_ny_download_af.sh └── merge_chroms.sh ├── LICENSE ├── README.md ├── assembly ├── n50.sh ├── platanus.sh └── spades.sh ├── bam ├── bam.coverage.bamstats04.sh ├── bam.coverage.base_wise.stat.py ├── bam.coverage.gene_wise.sh ├── bam.coverage.less20.sh ├── bam.coverage.median.sh ├── bam.coverage.per_exon.sh ├── bam.coverage.prepare_bed.sh ├── bam.coverage.sh ├── bam.raw_coverage.sh ├── bam.read_count.sh ├── bam.remove_region.sh ├── bam.sort.sh ├── bam.subsample.sh └── bam2fq.sh ├── barcodes ├── fgbio.sh ├── fix_novaseq_indrops3.awk ├── fix_novaseq_indrops3.slurm.sh ├── indrops3_bcl2fastq.sh ├── twinstrand_discover_umi.sh └── twinstrand_umi_prep.sh ├── basespace ├── basespace_download_dataset.sh ├── basespace_sample_run.sh ├── bcl2fastq.sh ├── pon_generation.md └── pon_subset.py ├── bcbio ├── bcbio.alignment.yaml ├── bcbio.custom_genome.sh ├── bcbio.mirna.athaliana.yaml ├── bcbio.mirna.potato.yaml ├── bcbio.mirna.soybean.yaml ├── bcbio.rnaseq.yaml ├── bcbio.sh ├── bcbio.sv.yaml ├── bcbio.upgrade.sh ├── bcbio.upgrade_star.sh ├── bcbio_nextgen_install.py ├── bcbio_scrnaseq.sh ├── bwa_umi.sh └── duplex_umi.yaml ├── blast ├── 08.blastn_xml.sh ├── blast.2coverage.pl ├── blast.add_taxonomy.sh ├── blast.fix_numhits.pl ├── blast.get_protein.sh ├── blast.get_subset_by_species_list.pl ├── blast.get_taxonomy_by_gene_id.sh ├── blast.get_taxonomy_by_protein_id.sh ├── blast.protein_name_by_gi.sh ├── blast.stat.sh ├── blast.xml2flat.pl ├── blast.xml2flat1.py ├── blast_psi.sh ├── blastn.sh └── blastn_xml.parse_example.py ├── clinvar ├── clinvar_download.sh ├── clinvar_mc_stats.sh ├── clinvar_missing.sh ├── clinvar_select_mc_pathogenic.sh ├── clinvar_select_pathogenic_reliable.sh └── clinvar_stats.sh ├── clusters ├── bcbio.ipython.o2.sh ├── o2.tar.sh ├── qsub.sk.sh ├── sbatch.array.o2.sh ├── sbatch.o2.sh └── usage_stats.sh ├── coverage ├── bamstats05.sh └── mark_duplicates.sh ├── cram ├── cram2bam.sh └── cram2fastq.sh ├── crispr ├── crispresso.sh ├── crispresso_wgs.sh ├── extract_reads.py ├── find_proximal.py ├── process.sh └── scripts.sh ├── dragen ├── dragen_rnaseq.sh ├── dragen_rnaseq_3pass.sh ├── dragen_rnaseq_hg19.sh ├── dragen_somatic.sh └── gather_fusion_stats.sh ├── fastq ├── fastq-join ├── fastq.blast_trimmer.pl ├── fastq.fastqc_get_adapters.sh ├── fastq.fna2fastq.pl ├── fastq.get_phred_scale.sh ├── fastq.get_read.pl ├── fastq.get_read_make_index.pl ├── fastq.join.sh ├── fastq.mp_check_adapter.pl ├── fastq.mp_process.sh ├── fastq.nreads.sh ├── fastq.qc.2files.pbs ├── fastq.qc.2files.sh ├── fastq.qc.pbs ├── fastq.remove_duplicates.sh ├── fastq.reverse_complement.pl ├── fastq.split.sh ├── fastq.sra2fq.sh ├── fastq.subsampler.py ├── fastq.trim.pbs ├── fastq.trim_left.pl ├── fastq.trim_right.pl ├── fastq.trim_single.sh ├── fastq2bin ├── fastq2bin.cpp ├── fastq2fasta ├── fastq2fasta.sh ├── fastq2to1.pl ├── fastq2to1.py └── fastqc.sh ├── filesystem ├── check_cmp_dir.sh └── check_md5_dir.py ├── fusions ├── arriba.sh └── gather_stats.sh ├── gatkcnv ├── 01.preprocess_intervals.sh ├── 02.annotate_gc.sh ├── 03.collect_read_counts.sh ├── 04.create_pon.sh ├── 05.denoise_read_counts.sh ├── 06.hdf5.non_zero.py ├── 07.plot_denoised.sh ├── 08.allelic_counts.sh ├── 09.model_segments.sh ├── 10.call_copy_ratio.sh ├── 11.plot_modeled_segments.sh ├── 11.plot_modeled_segments_ton.sh └── gatkcnv.md ├── gene_panels ├── README.md ├── canonical_cancer.txt ├── canonical_cancer_99.txt ├── cheo_act.bed ├── cheo_act.csv ├── cheo_act.issues ├── cheo_id.bed ├── cheo_id.csv ├── cheo_id.issues ├── cheo_mito.bed ├── cheo_mito.csv ├── cheo_myopathy.bed ├── cheo_myopathy.csv ├── cheo_scid.bed ├── cheo_scid.csv ├── cheo_scid.issues ├── chip.gene_name.csv ├── chip.grch37.bed ├── chip.grch37.csv ├── chip.grch37.unsorted.bed ├── chip.hg38.bed ├── chip.hg38.csv ├── chip.hg38.exons.bed ├── chip.hg38.exons.merged.bed ├── chip.hg38.exons.padded.bed ├── chip.hg38.exons.padded.sorted.bed ├── chip.hg38.unsorted.bed ├── dplm_recurrent_fever_syndrome.csv ├── dplm_recurrent_fever_syndrome.sorted.ensg ├── genedx_brain_malformations.txt ├── genes.R ├── genes_distribution.pdf ├── genes_distribution.png ├── genomics_england_periodic_fever_syndromes.csv ├── genomics_england_periodic_fever_syndromes.sorted.ensg ├── genomics_england_primary_immunodeficiency.csv ├── genomics_england_primary_immunodeficiency.sorted.ensg ├── genomics_england_primary_immunodeficiency1.csv ├── gonorazky2019_muscular_genes.csv ├── grch37.mt.bed ├── hiraki.dna_repair.csv ├── hiraki.mas.sorted.ensgid ├── hiraki_lupus_eastasians_gwas.csv ├── hiraki_lupus_langefeld_gwas.csv ├── hiraki_mas.bed ├── hiraki_mas.csv ├── immunopanels.R ├── mouse.protein_coding.csv ├── panel_filter.R ├── panel_filter.tcag.R ├── panel_filter.tcag.sv.R └── twist.test.bed ├── journal_club ├── README.md ├── cnv.md └── journals.md ├── kraken ├── kraken.sh ├── kraken_quick.sh ├── kraken_single.sh └── kraken_summarise.sh ├── liftover ├── 01.download_chain.sh ├── 02.lift_over_vcf.sh ├── 02.lift_over_vcf_gz.sh ├── 03.lift_over_cfvcf.sh └── paired_lift_over.py ├── omim ├── README.md ├── omim_extract_inheritance.py ├── omim_inheritance2025.png └── omim_plot_inheritance_dictionary.R ├── paml ├── codeml.template ├── fasta2phy.pl ├── fasta2phylip.pl ├── paml.sh └── paml_parse.pl ├── phylogeny ├── modeltest.sh └── mrbayes.sh ├── phylogicndt └── purecn2phylogicndt.R ├── purecn ├── .profile_example ├── 01.UCSC_repeats.R ├── 01.download_references.sh ├── 0X.interval_file.sh ├── 0X.normal_db.sh ├── 0X.preprocess_intervals.sh ├── 0X.purecn.sh ├── 142.genomics_Db.sh ├── 142.somatic_pon.sh ├── 21.bed2interval_list.sh ├── 22.gc_annotation.sh ├── 22.process_intervals.sh ├── 23.collect_read_counts.sh ├── 24.cnv_pon.sh ├── 3.snv_ton.sh ├── 31.mutect2.sh ├── 32.gc_coverage.sh ├── 4.cnv_ton.sh ├── 41.combine_variants.sh ├── 51.normal_db.sh ├── 61.mutect2wpon.sh ├── 62.filter_mutect.sh ├── 71.purecn.sh ├── 8.signatures.sh ├── ERBB2.tsv ├── PTEN.tsv ├── README.md ├── filter_results.sh ├── gather_gene_level_table.sh └── get_mapd.R ├── quality_control ├── fastp.sh ├── fastp.umi_processing.sh ├── fastqc.slurm.sh ├── preseq.sh ├── prinseq-lite.pl ├── prinseq.sh ├── somalier.sh └── twin_umi.sh ├── scripts ├── AdapterRemoval ├── alignment.UCSC.dm6droSim1.sh ├── alignment.avr_pw_dist.pl ├── alignment.check_3x.sh ├── alignment.check_conservative_site.sh ├── alignment.consensus.2seq.pl ├── alignment.consensus.pl ├── alignment.count_gaps.sh ├── alignment.detect_stops.pl ├── alignment.fa2fasta.pl ├── alignment.fasta2slice.pl ├── alignment.filter_not3x.sh ├── alignment.fix_ends.sh ├── alignment.muscle.sh ├── alignment.nucleotide_diversity.pl ├── alignment.occupancy.pl ├── alignment.protein2dna.sh ├── alignment.remove_ambiguity.pl ├── alignment.remove_cons_n_gaps.pl ├── alignment.remove_gaps.pl ├── alignment.remove_seqs_having_stops.pl ├── alignment.remove_sp4occupancy.pl ├── alignment.remove_stops_n_gaps.pl ├── alignment.remove_stops_n_gaps2.pl ├── alignment.reverse_complement.pl ├── alignment.sort_by_id.pl ├── alignment.substitution_profile.pl ├── alignment.tr_trv.pl ├── alignments.concatenate.pl ├── alignments.concatenate1.pl ├── bcbio.get_illimina_exome_bed.sh ├── bcbio.mirna.12samples.csv ├── bcbio.mirna.athaliana.35samples.csv ├── bcbio.mirna.athaliana.prepare_config.sh ├── bcbio.mirna.gff2gtf.py ├── bcbio.mirna.prepare.athaliana.sh ├── bcbio.mirna.prepare.glymax.sh ├── bcbio.mirna.prepare.soltub.sh ├── bcbio.mirna.prepare_config.sh ├── bcbio.prepare_samples.sh ├── bcbio.rnaseq.get_tmp.sh ├── bcbio.rnaseq.get_tpm.sh ├── bcl2fq.sh ├── bed.sort.sh ├── bootstrap.mean_and_CI.pl ├── bunzip2.pbs ├── bwa.mem.sh ├── bzip2.sh ├── cheo.filtered_vcf.sh ├── cheo.get_new_variants.pl ├── cheo.naming1.sh ├── cheo.naming2.sh ├── cheo.vcf.compare2.sh ├── cheo.vcf.comparison.sh ├── chromosome_names.txt ├── dexpression.athaliana.R ├── du.pbs ├── epistasis.calc_k.sh ├── epistasis.calc_r.sh ├── epistasis.sh ├── epistasis2.cpp ├── fasta.get_sequence_chunk.py ├── fasta.someRecordsField.pl ├── fasta2nexus.py ├── gam.blastp.pbs ├── gam.blastp.sh ├── gam.filter.sh ├── gam.ortho.sh ├── gam.orthomcl.make_alignments.pl ├── gam.remove_contamination.sh ├── gdrive.get_file.sh ├── gemini.R ├── go.B2G4pipe.pbs ├── go.adapter_removal.sh ├── go.blastn.pbs ├── go.blastx.pbs ├── go.blastx.sh ├── go.bowtie2.exact.sh ├── go.bowtie2.sh ├── go.bowtie2_single.sh ├── go.dnaseq.pbs ├── go.fastq-dump.pbs ├── go.gatk.all.pbs ├── go.gatk1.pbs ├── go.gatk2.pbs ├── go.gatk3.pbs ├── go.golipour.pbs ├── go.golipour1.pbs ├── go.golipour2.pbs ├── go.gzip.pbs ├── go.hyphy.sh ├── go.hyphy.sh.input ├── go.kalign.sh ├── go.mafft.sh ├── go.novoalign.sh ├── go.oases.sh ├── go.raxml.pbs ├── go.raxml_boot1000.pbs ├── go.repeatscout.sh ├── go.snpeff.html.pbs ├── go.snpeff.html.sh ├── go.snpeff.pbs ├── go.snpeff.sh ├── go.tba.sh ├── go.trinity.pbs ├── go.velvet.pbs ├── goblastp_xml.sh ├── golipour.split.sh ├── gunzip.pbs ├── gvcf2vcf.sh ├── gzip.slurm.sh ├── hla.athlates.sh ├── hyphy.json2sites.sh ├── illumina.adapters.fasta ├── incumbent.calc_syn_div.pl ├── incumbent.fasta2fourfold.pl ├── incumbent.fasta2nondegenerate.pl ├── incumbent.fasta2nondegenerate1.pl ├── incumbent.fasta2nondegenerate3.pl ├── incumbent.nondeg2noncons.sh ├── incumbent.procedure3.sh ├── ips.t_assym.sh ├── kondrashev.positiveSelectionSimulation07.c ├── lobstr.sh ├── lobstr_single_end.sh ├── maf2fasta.prepare.pl ├── md5sum.sh ├── mh.filter.sh ├── mh.procedure.sh ├── mirna.dexpression.edgeR.R ├── mirna.exploratory_analysis.rmd ├── mirna.plant.shortstask.pbs ├── muscle.stabilize.py ├── newbler.get_longest_isotig.pl ├── qhost ├── quse.sh ├── raxml.avx.bootstrap.pbs ├── raxml.boot.outgroup.pbs ├── raxml.rapid_bootstrap.pbs ├── raxml.sh ├── remap.sed ├── rival.sh ├── rnaseq.call_mutations.sh ├── rnaseq.call_mutations_mouse.sh ├── rnaseq.dexpression.katie.R ├── rnaseq.dexpression.vdk.R ├── rnaseq.exon_usage.dexseq.R ├── rnaseq.qorts.make_junction_track.sh ├── rnaseq.qorts.makeflatgff.sh ├── rnaseq.qorts.merge_novel_splices.sh ├── rnaseq.qorts.qc.sh ├── rnaseq.qorts.sublist.pl ├── rnaseq.splicing.junction_seq.R ├── rnaseq.splicing.junction_seq.sh ├── rnaseq.splicing.junctionseq.decoder.txt ├── seqtk ├── summary_table.py ├── tar.sh ├── tba.prepare.pl ├── tcag_sftp.sh ├── test.pbs ├── tree ├── tree.get_species.sh ├── tree.newick2nexus ├── tree.nexus2newick ├── tree.raxml_boot.sh ├── tree.round_branch_lengths.sh ├── tree.substitute_names.pl ├── trimadap ├── trimadap.readme ├── trinity.cds_stat.sh ├── trinity.extract_cds.sh ├── trinity.get_longest_isoform.pl ├── trinity.rsem_expression.sh ├── unzip.pbs ├── variants.R ├── vcf.compare.sh ├── vcf.compare.snps_per_gene.sh ├── vcf.filter.sh ├── vcf.get_context.pbs ├── vcf.get_context.sh ├── vcf.split_multisample_vcf.sh ├── vcf2fasta.sh ├── vcf2spectrum.sh ├── vcf2txt.sh └── zcat.pbs ├── variants ├── call_in_window.sh ├── fgbio.sh ├── gatkcnv2tsv.sh ├── get_af.sh ├── get_sor.sh ├── gvcf2vcf.sh ├── 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