├── .gitattributes ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── Rulegraph.png ├── Tools_config ├── Biowulf_Strelka.config.ini ├── Biowulf_defuse.config_hg19_ens69.txt ├── Biowulf_snpEff.config ├── TGen_Strelka.config.ini ├── TGen_defuse.config_hg19_ens69.txt └── TGen_snpEff.config ├── bedFileFormatting ├── formatBed.sh └── ref │ ├── Exons_06302016_ensembl_formatted_noUTR.merged.bed │ ├── Exons_06302016_refseq_formatted_noUTR.merged.bed │ └── ucsc.hg19.genome ├── config ├── config_annotation.json ├── config_cluster.json ├── config_common.json ├── config_common_biowulf.json └── config_common_tgen.json ├── dag.png ├── launch ├── ngs_pipeline.rules ├── ruleBook ├── Actionable.rules ├── Consolidate.rules ├── HotSpot_Pileup.rules ├── MethlySeq.rules ├── NeoAntigen.rules ├── STAR.rules ├── Sequenza.rules ├── UnionSomaticMutations.rules ├── annot.1.rules ├── annot.rules ├── bam2mpg.rules ├── bamUtil.rules ├── cnvkit.rules ├── failedExon.rules ├── gatk_RNASeq.rules ├── haplotypeCaller.rules ├── hsMetrix.rules ├── ideogram.rules ├── mutationalSignature.rules ├── platypus.rules ├── plots.rules ├── readDepth.rules ├── rnaseqQC.rules ├── rnaseq_pipeline.rules ├── universal.rules └── verifyBamID.rules ├── samplesheet.json ├── samplesheet.txt ├── scripts ├── Actionable.v3.pl ├── ActionableFusion.v1.pl ├── AddGene.pl ├── AddSampleType.pl ├── CombineAnnotations.pl ├── ExpressedMutations.pl ├── GeneAnnotation.pl ├── GeneAnnotation.v1.pl ├── ListStatistics.R ├── MakeAnnotationInputs.pl ├── MergeCalls.pl ├── MovingWindow.pl ├── ParsePPH2.pl ├── ParseSIFT.pl ├── ProteinCoding.pl ├── ProteinCodingRare.pl ├── QC_stats_Final.py ├── SJDB.awk ├── TableAnno.sh ├── UnionSomaticCalls.pl ├── addAnnotation.pl ├── addAnnotations2vcf.pl ├── addAttributes.pl ├── addFS.pl ├── awk_sort_withHeader.awk ├── block_for_jobid.pl ├── boxplot.R ├── circos.R ├── consensusHLA.pl ├── consensusSomaticVCF.pl ├── copyNumber.sh ├── coverage.R ├── coveragePlot.R ├── exon_exp.sh ├── failed_Exon_Final.pl ├── featureCounts.R ├── featureCounts.v2.R ├── filterCNV.pl ├── filterVariants.pl ├── filterVariants.v1.pl ├── findAlreadyExistingVariants.pl ├── fpkm2log2_fpkm.pl ├── germlineOnly.pl ├── hotspot_mpileup.pl ├── ideogram.R ├── igv_snapshot.rules ├── jobscript.sh ├── makeDBVariantFile.pl ├── makeJSON.py ├── makeQC.pl ├── meltSnpEff.pl ├── mpileup.pl ├── mutationSignature.R ├── parallel ├── process_pVACSeq.pl ├── rnaseqQC.pl ├── run_sequenza_pipeline.R ├── scoreGenotyes.pl ├── sequenza-utils.py ├── stats2Table.py ├── transcript_coverage.R ├── transformlog2_FPKM.py ├── tsv2html.final.sh ├── tsv2html.sh ├── vcf-filter.pl ├── vcf2genotype.pl ├── vcf2loh.pl ├── vcf2txt.pl └── vcfOrderCol.R └── submit_snakemake.sh /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patidarr/ngs_pipeline/HEAD/.gitattributes -------------------------------------------------------------------------------- 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