bin/configManta.py
bin/configManta.py.ini
bin/runMantaWorkflowDemo.py
lib/python/checkChromSet.py
lib/python/checkChromSet.pyc
lib/python/configBuildTimeInfo.py
lib/python/configBuildTimeInfo.pyc
lib/python/configureOptions.py
lib/python/configureOptions.pyc
lib/python/configureUtil.py
lib/python/configureUtil.pyc
lib/python/estimateHardware.py
lib/python/estimateHardware.pyc
lib/python/makeRunScript.py
lib/python/makeRunScript.pyc
lib/python/mantaOptions.py
lib/python/mantaOptions.pyc
lib/python/mantaWorkflow.py
lib/python/mantaWorkflow.pyc
lib/python/pyflow/pyflow.py
lib/python/pyflow/pyflow.pyc
lib/python/pyflow/pyflowConfig.py
lib/python/pyflow/pyflowConfig.pyc
lib/python/pyflow/pyflowTaskWrapper.py
lib/python/pyflow/pyflowTaskWrapper.pyc
lib/python/sharedWorkflow.py
lib/python/sharedWorkflow.pyc
lib/python/workflowUtil.py
lib/python/workflowUtil.pyc
libexec/CheckSVLoci
libexec/DumpSVLoci
libexec/EstimateSVLoci
libexec/GenerateSVCandidates
libexec/GetAlignmentStats
libexec/GetChromDepth
libexec/MergeAlignmentStats
libexec/MergeSVLoci
libexec/SummarizeAlignmentStats
libexec/SummarizeSVLoci
libexec/TestAssembler
libexec/bgzip
libexec/cat.py
libexec/cat.pyc
libexec/convertInversion.py
libexec/convertInversion.pyc
libexec/denovo_scoring.py
libexec/denovo_scoring.pyc
libexec/extractSmallIndelCandidates.py
libexec/extractSmallIndelCandidates.pyc
libexec/htsfile
libexec/mergeBam.py
libexec/mergeBam.pyc
libexec/mergeChromDepth.py
libexec/mergeChromDepth.pyc
libexec/ploidyFilter.py
libexec/ploidyFilter.pyc
libexec/samtools
libexec/sortBam.py
libexec/sortBam.pyc
libexec/sortEdgeLogs.py
libexec/sortEdgeLogs.pyc
libexec/sortVcf.py
libexec/sortVcf.pyc
libexec/tabix
libexec/updateSampleFTFilter.py
libexec/updateSampleFTFilter.pyc
libexec/vcfCmdlineSwapper.py
libexec/vcfCmdlineSwapper.pyc
share/CHANGELOG.md
share/COPYRIGHT.txt
share/LICENSE.txt
share/demo/manta/README.md
share/demo/manta/data/G15512.HCC1954.1.COST16011_region.bam
share/demo/manta/data/G15512.HCC1954.1.COST16011_region.bam.bai
share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam
share/demo/manta/data/HCC1954.NORMAL.30x.compare.COST16011_region.bam.bai
share/demo/manta/data/Homo_sapiens_assembly19.COST16011_region.fa
share/demo/manta/data/Homo_sapiens_assembly19.COST16011_region.fa.fai
share/demo/manta/expectedResults/somaticSV.vcf.gz
