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