README.md
setup.py
BEDTools/BEDTools.py
BEDTools/__init__.py
BamQC/BamQC.py
BamQC/__init__.py
PyHive/Hive.py
PyHive/__init__.py
PyHive/Attribute/StoreAttribute.py
PyHive/Attribute/__init__.py
PyHive/Bam/RunSamToolsIndex.py
PyHive/Bam/RunSamToolsMerge.py
PyHive/Bam/__init__.py
PyHive/BamQC/RunChkIndelRg.py
PyHive/BamQC/RunPicardOnWESfile.py
PyHive/BamQC/RunPicardOnWGSfile.py
PyHive/BamQC/RunVerifyBamId.py
PyHive/BamQC/__init__.py
PyHive/Factories/BeagleChunkFactory.py
PyHive/Factories/ChrFactory.py
PyHive/Factories/CoordFactory.py
PyHive/Factories/ShapeitChunkFactory.py
PyHive/Factories/SliceFactory.py
PyHive/Factories/SplitVCF.py
PyHive/Factories/SplitVCFintoChros.py
PyHive/Factories/TransposeBam.py
PyHive/Factories/__init__.py
PyHive/File/CompressBybgzip.py
PyHive/File/ShortenFilePaths.py
PyHive/File/ShortenFiles.py
PyHive/File/SplitFile.py
PyHive/File/StoreFile.py
PyHive/File/__init__.py
PyHive/Seed/SeedFile.py
PyHive/Seed/SeedShapeit.py
PyHive/Seed/SeedVCFIntegration.py
PyHive/Seed/__init__.py
PyHive/TOPMed/IndexBam.py
PyHive/TOPMed/MarkDuplicates.py
PyHive/TOPMed/RnaseqcCounts.py
PyHive/TOPMed/Rsem.py
PyHive/TOPMed/SamtoolsQuickcheck.py
PyHive/TOPMed/Star.py
PyHive/TOPMed/__init__.py
PyHive/VariantCalling/BCFTools_caller.py
PyHive/VariantCalling/GATK_HC.py
PyHive/VariantCalling/GATK_UG.py
PyHive/VariantCalling/__init__.py
PyHive/Vcf/BcftoolsVcfNorm.py
PyHive/Vcf/CombineVariants.py
PyHive/Vcf/NormVcf.py
PyHive/Vcf/VariantsToAllelicPrimitives.py
PyHive/Vcf/VcfAllelicPrim.py
PyHive/Vcf/VcfCombine.py
PyHive/Vcf/VcfConcat.py
PyHive/Vcf/VcfIxByTabix.py
PyHive/Vcf/VcfReheader.py
PyHive/Vcf/VcfReplaceChrNames.py
PyHive/Vcf/__init__.py
PyHive/Vcf/convertPL2GL.py
PyHive/Vcf/dropInfo.py
PyHive/VcfFilter/ApplyRecalibration.py
PyHive/VcfFilter/BcftoolsFilter.py
PyHive/VcfFilter/SelectVariants.py
PyHive/VcfFilter/SplitVariants.py
PyHive/VcfFilter/SubsetVcfWithBed.py
PyHive/VcfFilter/SubsetVcfWithRegion.py
PyHive/VcfFilter/VariantRecalibrator.py
PyHive/VcfFilter/__init__.py
PyHive/VcfIntegration/CollectRawF.py
PyHive/VcfIntegration/SNPTools_bamodel.py
PyHive/VcfIntegration/SNPTools_poprob.py
PyHive/VcfIntegration/SNPTools_prob2vcf.py
PyHive/VcfIntegration/__init__.py
PyHive/VcfIntegration/run_Beagle.py
PyHive/VcfIntegration/run_Shapeit.py
PyHive/VcfIntegration/run_Shapeit_convert2vcf.py
PyHive/VcfIntegration/run_ligateHAPLOTYPES.py
PyHive/VcfIntegration/run_prepareGenFromBeagle4.py
PyHive/VcfQC/BcftoolsStats.py
PyHive/VcfQC/ChrosInVcf.py
PyHive/VcfQC/CollectVariantCallingMetrics.py
PyHive/VcfQC/GTConcordance.py
PyHive/VcfQC/PlotVariantDensity.py
PyHive/VcfQC/VariantsInRegions.py
PyHive/VcfQC/__init__.py
ReseqTrackDB/ReseqTrackDB.py
ReseqTrackDB/__init__.py
ReseqTrackDB/main.py
SequenceIndex/SequenceIndex.py
SequenceIndex/__init__.py
SequenceIndex/main.py
Utils/RunProgram.py
Utils/RunSingularity.py
Utils/__init__.py
VCF/VcfNormalize.py
VCF/VcfQC.py
VCF/VcfUtils.py
VCF/__init__.py
VCF/VCFIntegration/Beagle.py
VCF/VCFIntegration/SNPTools.py
VCF/VCFIntegration/Shapeit.py
VCF/VCFIntegration/__init__.py
VCF/VCFfilter/BCFTools.py
VCF/VCFfilter/GATK.py
VCF/VCFfilter/MLclassifier.py
VCF/VCFfilter/__init__.py
VariantCalling/BCFTools.py
VariantCalling/GATK.py
VariantCalling/__init__.py
igsr_analysis.egg-info/PKG-INFO
igsr_analysis.egg-info/SOURCES.txt
igsr_analysis.egg-info/dependency_links.txt
igsr_analysis.egg-info/requires.txt
igsr_analysis.egg-info/top_level.txt
p3/__init__.py
p3/p3BAMQC.py