| Directory automation |
| Directory CNV |
| Directory data |
| Directory galaxy |
| Directory libraries/lib64/python2.7/site-packages |
| Directory mutation_signature_scripts |
| Directory pipelines |
| Directory platypus-pmac-wrapper |
| Directory super_wrapper_scripts |
| Directory util |
| File addEncodeBlacklist.py | 1.88 KB |
| File addGcContentToBed.py | 1.50 KB |
| File addGeneData.pl | 2.31 KB |
| File addReadGroupToBam.sh | 328 B |
| File addRepeatMaskerToTsv.sh | 1.25 KB |
| File addSampleCountsPerVariant.py | 1.71 KB |
| File addSymToDepthOfCoverage.py | 650 B |
| File adtex_make_baf.R | 3.02 KB |
| File annotateBedFile.pl | 4.84 KB |
| File annotateByEnsId.pl | 4.75 KB |
| File annotateByGeneName.pl | 5.02 KB |
| File annotOncotatorBatch.py | 5.43 KB |
| File bam2fa.sh | 317 B |
| File blatAgainstBam.py | 986 B |
| File combine_performance.py | 2.10 KB |
| File combineStandarFamilialVariants.py | 3.93 KB |
| File combineStandarSomaticVariants.py | 3.84 KB |
| File CompileMasterVariantFile_Germline.py | 3.96 KB |
| File create_roi.py | 503 B |
| File createIndexes.py | 6.86 KB |
| File dos2unix.sh | 34 B |
| File edgeR.pl | 12.65 KB |
| File ensembl.config_file | 552 B |
| File ensembl.config_file_mouse | 553 B |
| File ensembl73_perl5lib.sh | 686 B |
| File export_gatk_variants_to_columns.py | 1.64 KB |
| File extract_seq.pl | 1.96 KB |
| File extract_seq_byFile.pl | 2.57 KB |
| File extractRegions.py | 3.93 KB |
| File filterTSV.py | 3.99 KB |
| File geneCoveragePerSample.py | 7.79 KB |
| File getCADD_byAnnovar.sh | 740 B |
| File getCADD_byTabix.py | 2.31 KB |
| File getExAC_byTabix.py | 3.44 KB |
| File getFilePaths.py | 1.71 KB |
| File getUniqueVariants.py | 1.27 KB |
| File groom_all.sh | 946 B |
| File intersectVCF.py | 2.88 KB |
| File lookupAndAppend.py | 2.04 KB |
| File mergeBedCov.py | 2.50 KB |
| File mergeTSVRowsByValues.py | 3.63 KB |
| File mergeVariantInfo.py | 1.74 KB |
| File mobas.py | 4.38 KB |
| File mouseHumanSymMap.py | 2.01 KB |
| File mouseHumanSymMapHUGO.py | 2.28 KB |
| File mutation_signature.sh | 782 B |
| File plot_ADTEx.R | 4.86 KB |
| File prepareBed_extendAndMergeRegions.R | 2.49 KB |
| File prepareSomaticSampleSheet.py | 4.43 KB |
| File README.md | 106 B |
| File reorderTSVColumns.py | 1.34 KB |
| File reorderTSVColumnsByNames.py | 3.29 KB |
| File retrieve_reads_from_variants.py | 4.08 KB |
| File seqQCpipe.py | 8.96 KB |
| File seqQCpipe_v2.py | 9.56 KB |
| File somaticFilterFromCombinedVCF.py | 1.09 KB |
| File sortBedV.sh | 34 B |
| File splitColumnAD.py | 709 B |
| File splitFamilialVariantFile.py | 3.84 KB |
| File splitVcfBySample.py | 987 B |
| File subtractVCF.py | 1.49 KB |
| File tsv2vcf.py | 978 B |
| File vcf-trimIUPAC.py | 648 B |
| File vs2vcf.pl | 1.20 KB |
