├── .github ├── dependabot.yml └── workflows │ ├── docker.yml │ ├── gradle.yml │ └── release.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── settings.gradle └── src ├── main ├── java │ └── com │ │ └── github │ │ └── discvrseq │ │ ├── Main.java │ │ ├── tools │ │ ├── DiscvrSeqDevProgramGroup.java │ │ ├── DiscvrSeqInternalProgramGroup.java │ │ ├── DiscvrSeqProgramGroup.java │ │ └── VariantManipulationProgramGroup.java │ │ ├── util │ │ ├── CigarPositionIterable.java │ │ ├── CsvUtils.java │ │ ├── NaturalSortComparator.java │ │ ├── SamUtils.java │ │ ├── SequenceMatcher.java │ │ ├── VariableOutputUtils.java │ │ └── help │ │ │ └── DISCVRSeqHelpDoclet.java │ │ └── walkers │ │ ├── AnnotateNovelSites.java │ │ ├── AppendGenotypes.java │ │ ├── BackportLiftedVcf.java │ │ ├── ClinvarAnnotator.java │ │ ├── ClipOverlappingAlignments.java │ │ ├── CrossSampleGenotypeComparison.java │ │ ├── ExtendedFuncotator.java │ │ ├── ExtendedMultiVariantWalkerGroupedOnStart.java │ │ ├── FindGenomeDifferences.java │ │ ├── GenotypeFilterBySample.java │ │ ├── GroupCompare.java │ │ ├── IdentifySoftClippedLoci.java │ │ ├── ImmunoGenotyper.java │ │ ├── MendelianViolationReport.java │ │ ├── MergeFastqReads.java │ │ ├── MergeVariantSites.java │ │ ├── MergeVcfsAndGenotypes.java │ │ ├── MultiSourceAnnotator.java │ │ ├── MultipleAllelesAtLoci.java │ │ ├── OutputVariantsStartingInIntervals.java │ │ ├── PrintReadBackedHaplotypes.java │ │ ├── PrintReadsContaining.java │ │ ├── RemoveAnnotations.java │ │ ├── SampleSpecificGenotypeFiltration.java │ │ ├── Save10xBarcodes.java │ │ ├── SplitVcfBySamples.java │ │ ├── Summarize10xAlignments.java │ │ ├── SummarizeGenotypeQuality.java │ │ ├── VariantConcordanceScore.java │ │ ├── VcfComparison.java │ │ ├── VcfFilterComparison.java │ │ ├── VcfToLuceneIndexer.java │ │ ├── annotator │ │ ├── DiscvrVariantAnnotator.java │ │ ├── GenotypeConcordance.java │ │ ├── GenotypeConcordanceArgumentCollection.java │ │ ├── GenotypeConcordanceBySite.java │ │ ├── Impact.java │ │ ├── MendelianViolationArgumentCollection.java │ │ ├── MendelianViolationBySample.java │ │ ├── MendelianViolationCount.java │ │ ├── MinorAlleleFrequency.java │ │ ├── RefAlleleFrequency.java │ │ ├── RefAlleleFrequencyArgumentCollection.java │ │ └── SVType.java │ │ ├── tagpcr │ │ ├── InsertDescriptor.java │ │ ├── InsertJunctionDescriptor.java │ │ ├── IntegrationSiteMapper.java │ │ └── SequenceDescriptor.java │ │ └── variantqc │ │ ├── BarPlotReportDescriptor.java │ │ ├── Contig.java │ │ ├── ExtendedVariantEvalEngine.java │ │ ├── GATKReportTableTransformer.java │ │ ├── HtmlGenerator.java │ │ ├── InfoFieldEvaluator.java │ │ ├── PivotingTransformer.java │ │ ├── ReportDescriptor.java │ │ ├── SectionJsonDescriptor.java │ │ ├── TableReportDescriptor.java │ │ └── VariantQC.java └── resources │ └── com │ └── github │ └── discvrseq │ ├── util │ └── docTemplates │ │ ├── README.md │ │ ├── _config.yml │ │ ├── common.html │ │ ├── generic.index.template.html │ │ ├── generic.template.html │ │ ├── images │ │ └── variantQC_ExampleReport.jpg │ │ ├── index.md │ │ ├── resources │ │ ├── genomeRequirements.html │ │ └── variantQCSampleReport.html │ │ └── stylesheet.css │ └── walkers │ ├── tagpcr │ ├── BxbI-attP.yml │ ├── Lentivirus.yml │ ├── esTag-PCR-PREDICT.yml │ └── pENTR-PB511-Repro.yml │ └── variantqc │ └── templates │ ├── assets │ ├── css │ │ ├── bootstrap.min.css │ │ ├── default_multiqc.css │ │ └── font.css │ ├── fonts │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ └── glyphicons-halflings-regular.woff2 │ └── js │ │ ├── multiqc.js │ │ ├── multiqc_plotting.js │ │ ├── multiqc_tables.js │ │ ├── multiqc_toolbox.js │ │ ├── packages │ │ ├── FileSaver.min.js │ │ ├── bootstrap.min.js │ │ ├── chroma.min.js │ │ ├── clipboard.min.js │ │ ├── highcharts.exporting.js │ │ ├── highcharts.heatmap.js │ │ ├── highcharts.js │ │ ├── highcharts.offline-exporting.js │ │ ├── jquery-3.7.0.min.js │ │ ├── jquery-ui.min.js │ │ ├── jquery.tablesorter.min.js │ │ ├── lz-string.min.js │ │ └── numeral.min.js │ │ ├── shim.js │ │ └── summaryTable.js │ ├── template1.html │ └── template2.html └── test ├── java └── com │ └── github │ └── discvrseq │ └── walkers │ ├── AnnotateNovelSitesTest.java │ ├── AppendGenotypesIntegrationTest.java │ ├── BackportLiftedVcfIntegrationTest.java │ ├── BaseIntegrationTest.java │ ├── ClinvarAnnotatorIntegrationTest.java │ ├── ClipOverlappingAlignmentsIntegrationTest.java │ ├── CrossSampleGenotypeComparisonIntegrationTest.java │ ├── ExtendedFuncotatorIntegrationTest.java │ ├── GenotypeFilterBySampleIntegrationTest.java │ ├── GroupCompareIntegrationTest.java │ ├── IdentifySoftClippedLociIntegrationTest.java │ ├── ImmunoGenotyperIntegrationTest.java │ ├── MendelianViolationReportIntegrationTest.java │ ├── MergeFastqReadsIntegrationTest.java │ ├── MergeVariantSitesIntegrationTest.java │ ├── MergeVcfsAndGenotypesIntegrationTest.java │ ├── MergeVcfsAndGenotypesUnitTest.java │ ├── MultiSourceAnnotatorIntegrationTest.java │ ├── MultipleAllelesAtLociIntegrationTest.java │ ├── OutputVariantsStartingInIntervalsIntegrationTest.java │ ├── PrintReadBackedHaplotypesIntegrationTest.java │ ├── PrintReadsContainingIntegrationTest.java │ ├── RemoveAnnotationsIntegrationTest.java │ ├── SampleSpecificGenotypeFiltrationIntegrationTest.java │ ├── Save10xBarcodesIntegrationTest.java │ ├── SplitVcfBySamplesIntegrationTest.java │ ├── Summarize10xAlignmentsIntegrationTest.java │ ├── SummarizeGenotypeQualityIntegrationTest.java │ ├── VariantConcordanceScoreIntegrationTest.java │ ├── VcfComparisonIntegrationTest.java │ ├── VcfFilterComparisonIntegrationTest.java │ ├── VcfToLuceneIndexerIntegrationTest.java │ ├── annotator │ └── DiscvrVariantAnnotatorIntegrationTest.java │ ├── tagpcr │ └── IntegrationSiteMapperIntegrationTest.java │ └── variantqc │ └── VariantQCIntegrationTest.java └── resources └── com └── github └── discvrseq ├── TestData ├── 10xTestData.sam ├── 155_pRR_Reporter_U24.dict ├── 155_pRR_Reporter_U24.fasta ├── 155_pRR_Reporter_U24.fasta.fai ├── AnnotateNovelSitesRef.vcf ├── AnnotateNovelSitesRef.vcf.idx ├── ClinvarAnnotator.vcf ├── ClinvarAnnotator.vcf.idx ├── GenotypeFilterBySampleBlacklist.bed ├── GenotypeFilterBySampleBlacklist.bed.idx ├── ImmunoGenotyper.qsort.bam ├── MendelianViolationEval.ped ├── MendelianViolationEval.vcf ├── MendelianViolationEval.vcf.idx ├── MendelianViolationRefGT.vcf ├── MendelianViolationRefGT.vcf.idx ├── Population_iv.overlapping.bam ├── Population_iv.overlapping.bam.bai ├── Rhesus_KIR_and_MHC_1.0.dict ├── Rhesus_KIR_and_MHC_1.0.fasta ├── Rhesus_KIR_and_MHC_1.0.fasta.fai ├── SVType.vcf ├── SVType.vcf.idx ├── SimpleExample.vcf.gz ├── SimpleExample.vcf.gz.tbi ├── SoftClipTestData.sam ├── basicVcf.vcf ├── basicVcf.vcf.idx ├── basicVcfFiltered.vcf ├── basicVcfFiltered.vcf.idx ├── clinvarV2.vcf ├── clinvarV2.vcf.idx ├── funcotator │ ├── funcotatorFields.txt │ ├── gencode │ │ └── hg19 │ │ │ ├── gencode.config │ │ │ ├── hg19.gtf │ │ │ ├── hg19.gtf.idx │ │ │ ├── hg19_transcript.dict │ │ │ ├── hg19_transcript.fa │ │ │ └── hg19_transcript.fa.fai │ ├── testSource │ │ └── hg19 │ │ │ ├── testSource.config │ │ │ ├── testSource.table │ │ │ └── testSource.table.idx │ └── vcfTestSource │ │ └── hg19 │ │ ├── vcfTestSource.config │ │ ├── vcfTestSource.vcf │ │ └── vcfTestSource.vcf.idx ├── genotypeAppend1.vcf ├── genotypeAppend1.vcf.idx ├── genotypeAppend2.vcf ├── genotypeAppend2.vcf.idx ├── genotypeFilterTest.vcf ├── genotypeFilterTest.vcf.idx ├── hg19micro.dict ├── hg19micro.fasta ├── hg19micro.fasta.fai ├── indexInput.vcf ├── indexInput.vcf.idx ├── lineageMap.txt ├── mergeVcf1.vcf ├── mergeVcf1.vcf.idx ├── mergeVcf2.vcf ├── mergeVcf2.vcf.idx ├── mergeVcf3.vcf ├── mergeVcf3.vcf.idx ├── mergeVcfWithAlts.vcf ├── mergeVcfWithAlts.vcf.idx ├── sample-map.txt ├── simpleTest.vcf ├── simpleTest.vcf.idx ├── softClipVariants.vcf ├── softClipVariants.vcf.idx ├── tagPcrTest.sam ├── variantConcordanceRef1.vcf ├── variantConcordanceRef1.vcf.idx ├── variantConcordanceRef2.vcf ├── variantConcordanceRef2.vcf.idx ├── vcfTwoContigs.vcf └── vcfTwoContigs.vcf.idx └── walkers ├── AnnotateNovelSites ├── missing.vcf ├── novel.vcf ├── output.vcf └── outputNoRef.vcf ├── AppendGenotypes └── append1.vcf ├── BackportLiftedVcf ├── backportLifted.vcf └── backportLiftedOutput.vcf ├── ClinvarAnnotator └── ClinvarAnnotatorOutput.vcf ├── ClipOverlappingAlignments ├── SIVmac239-overlap.bed ├── SIVmac239-overlap.bed.idx ├── SIVmac239.dict ├── SIVmac239.fasta ├── SIVmac239.fasta.fai ├── clipInput.sam ├── expectedOutput.sam ├── expectedOutput.txt ├── expectedOutput2.sam ├── expectedOutput2.txt ├── intervals.bed ├── intervals.bed.idx └── testSAM.sam ├── CrossSampleGenotypeComparison ├── crossSampleGenotypeComparison.txt └── crossSampleGenotypeComparisonSummary.txt ├── ExtendedFuncotator └── funcotator1.vcf ├── GenotypeFilterBySample └── GenotypeFilterBySample.vcf ├── GroupCompare ├── groupCompareInput1.vcf ├── groupCompareInput1.vcf.idx ├── groupCompareOutput.vcf ├── groupCompareOutputWithRef.txt ├── groupCompareOutputWithRef.vcf ├── groupCompareRef.vcf └── groupCompareRef.vcf.idx ├── IdentifySoftClippedLoci ├── IdentifySoftClippedLoci.bed ├── IdentifySoftClippedLociFiltered.bed └── IdentifySoftClippedLociWithVcf.bed ├── ImmunoGenotyper ├── ImmunoGenotyperOutput.genotypes.txt ├── ImmunoGenotyperOutput.mismatches.txt ├── ImmunoGenotyperOutput.summary.txt ├── ImmunoGenotyperOutputMM.genotypes.txt ├── ImmunoGenotyperOutputMM.mismatches.txt ├── ImmunoGenotyperOutputMM.summary.txt ├── ImmunoGenotyperOutputNVP.genotypes.txt ├── ImmunoGenotyperOutputNVP.mismatches.txt └── ImmunoGenotyperOutputNVP.summary.txt ├── MendelianViolationReport └── expectedOutput.txt ├── MergeFastqReads ├── basicMergeTest.fastq └── mergeTestWithMinLength.fastq ├── MergeVariantSites └── merge1.vcf ├── MergeVcfsAndGenotypes ├── basicTest2Output.vcf ├── basicTest3Output.vcf └── basicTestOutput.vcf ├── MultiSourceAnnotator ├── cassandra.vcf ├── cassandra.vcf.idx ├── clinvar.vcf ├── clinvar.vcf.idx ├── liftoverRejects.vcf ├── liftoverRejects.vcf.idx ├── multiSourceInput.vcf ├── multiSourceInput.vcf.idx ├── multiSourceOutput.vcf └── multiSourceOutputSubsetArgs.vcf ├── MultipleAllelesAtLoci ├── MultipleAllelesAtLoci.bed └── MultipleAllelesAtLociFiltered.bed ├── OutputVariantsStartingInIntervals └── basicOutput.vcf ├── PrintReadBackedHaplotypes ├── basicTest.txt ├── filteredTest.txt └── filteredTest2.txt ├── PrintReadsContaining ├── ED1_R1.fastq ├── ED1_R2.fastq ├── ED2_R1.fastq ├── ED2_R2.fastq ├── fq1.fastq └── fq2.fastq ├── RemoveAnnotations ├── testBasicOperation.vcf └── testBasicOperationSitesOnly.vcf ├── SampleSpecificGenotypeFiltration ├── basicTestOut.vcf └── rgqTestOut.vcf ├── Save10xBarcodes └── output.txt ├── SplitVcfBySamples ├── mergeVcf3.1of2.vcf ├── mergeVcf3.1of2Discard.vcf ├── mergeVcf3.2of2.vcf ├── mergeVcf3.2of2Discard.vcf ├── mergeVcfWithAlts.1of2.vcf ├── mergeVcfWithAlts.2of2.vcf ├── mergeVcfWithAltsRemoveAlts.1of2.vcf ├── mergeVcfWithAltsRemoveAlts.2of2.vcf ├── outputVcf1.vcf ├── outputVcf2.vcf └── outputVcf3.vcf ├── Summarize10xAlignments └── basicTest.txt ├── SummarizeGenotypeQuality └── basicTest.txt ├── VariantConcordanceScore └── variantConcordanceOutput.txt ├── VcfComparison ├── missingSites.vcf ├── missingSites2.vcf ├── novelSites.vcf ├── novelSites2.vcf ├── vcfComparison.txt ├── vcfComparison2.txt ├── vcfComparisonSites.txt ├── vcfComparisonSites2.txt └── vcfComparisonWithNoCall.txt ├── VcfFilterComparison └── vcfFilterComparison.txt ├── VcfToLuceneIndexer └── luceneOutDir.stats.txt ├── annotator └── DiscvrVariantAnnotator │ ├── basicTestOutput.vcf │ ├── basicTestWithCustomAnnotationsOutput.vcf │ ├── basicTestWithRefAlleleFrequency.vcf │ └── svtypeOutput.vcf ├── tagpcr └── IntegrationSiteMapper │ ├── BasicTest-1.metrics.txt │ ├── 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