site_name: "Jvarkit"

repo_url: "https://github.com/lindenb/jvarkit"

repo_name: "GitHub"

docs_dir: docs

theme:

name: readthedocs

highlightjs: true

html_show_sourcelink: false

prev_next_buttons_location: both

nav:

- "jvarkit" : JvarkitCentral.md

- "addlinearindextobed" : AddLinearIndexToBed.md

- "allelefreqcalc" : AlleleFrequencyCalculator.md

- "almostsortedvcf" : AlmostSortedVcf.md

- "backlocate" : BackLocate.md

- "bam2fastq" : BamToFastq.md

- "bam2haplotypes" : BamToHaplotypes.md

- "bam2mnv" : BamToMNV.md

- "bam2raster" : Bam2Raster.md

- "bam2sql" : BamToSql.md

- "bam2svg" : BamToSVG.md

- "bam2wig" : Bam2Wig.md

- "bam2xml" : Bam2Xml.md

- "bamclip2insertion" : BamClipToInsertion.md

- "bamcmpcoverage" : BamCmpCoverage.md

- "bamliftover" : BamLiftOver.md

- "bammatrix" : BamMatrix.md

- "bamphased01" : BamPhased01.md

- "bamrenamechr" : ConvertBamChromosomes.md

- "bamslicebed" : BamSliceBed.md

- "bamstats04" : BamStats04.md

- "bamstats05" : BamStats05.md

- "bamtile" : BamTile.md

- "bamwithoutbai" : BamWithoutBai.md

- "barcodegenerator" : BarcodeGenerator.md

- "basecoverage" : BaseCoverage.md

- "batchigvpictures" : BatchIGVPictures.md

- "bcftoolsmergebest" : BCFToolsMergeBest.md

- "bed2vcf" : BedToVcf.md

- "bedcluster" : BedCluster.md

- "bedindextabix" : BedIndexTabix.md

- "bedliftover" : BedLiftOver.md

- "bedmergecnv" : BedMergeCnv.md

- "bednonoverlappingset" : BedNonOverlappingSet.md

- "bedremovebed" : BedRemoveBed.md

- "bedrenamechr" : BedRenameChromosomes.md

- "bigwigmerge" : BigwigMerge.md

- "bigwigtview" : BigWigTView.md

- "bioalcidaejdk" : BioAlcidaeJdk.md

- "biostar103303" : Biostar103303.md

- "biostar105754" : Biostar105754.md

- "biostar130456" : Biostar130456.md

- "biostar139647" : Biostar139647.md

- "biostar145820" : Biostar145820.md

- "biostar154220" : Biostar154220.md

- "biostar160470" : Biostar160470.md

- "biostar165777" : Biostar165777.md

- "biostar170742" : Biostar170742.md

- "biostar172515" : Biostar172515.md

- "biostar173114" : Biostar173114.md

- "biostar175929" : Biostar175929.md

- "biostar178713" : Biostar178713.md

- "biostar214299" : Biostar214299.md

- "biostar234081" : Biostar234081.md

- "biostar234230" : Biostar234230.md

- "biostar251649" : Biostar251649.md

- "biostar322664" : Biostar322664.md

- "biostar332826" : Biostar332826.md

- "biostar336589" : Biostar336589.md

- "biostar352930" : Biostar352930.md

- "biostar3654" : Biostar3654.md

- "biostar398854" : Biostar398854.md

- "biostar404363" : Biostar404363.md

- "biostar480685" : Biostar480685.md

- "biostar489074" : Biostar489074.md

- "biostar497922" : Biostar497922.md

- "biostar59647" : Biostar59647.md

- "biostar76892" : Biostar76892.md

- "biostar77288" : Biostar77288.md

- "biostar77828" : Biostar77828.md

- "biostar78285" : Biostar78285.md

- "biostar81455" : Biostar81455.md

- "biostar84452" : Biostar84452.md

- "biostar84786" : Biostar84786.md

- "biostar86363" : Biostar86363.md

- "biostar86480" : Biostar86480.md

- "biostar90204" : Biostar90204.md

- "biostar9462889" : Biostar9462889.md

- "biostar9469733" : Biostar9469733.md

- "biostar9501110" : Biostar9501110.md

- "biostar9556602" : Biostar9556602.md

- "biostar95652" : Biostar95652.md

- "biostar9566948" : Biostar9566948.md

- "blast2sam" : BlastToSam.md

- "blastfilterjs" : BlastFilterJS.md

- "blastmapannots" : BlastMapAnnotations.md

- "blastn2snp" : BlastNToSnp.md

- "builddbsnp" : BuildDbsnp.md

- "cmpbams" : CompareBams.md

- "cmpbams4" : CompareBams4.md

- "cmpbamsandbuild" : CompareBamAndBuild.md

- "cnvtview" : CnvTView.md

- "cnvvalidatorserver" : CNVValidatorServer.md

- "commbams" : CommBams.md

- "convertliftoverchain" : ConvertLiftOverChain.md

- "copynumber01" : CopyNumber01.md

- "coveragematrix" : CoverageMatrix.md

- "coverageplotter" : CoveragePlotter.md

- "coverageserver" : CoverageServer.md

- "cytoband2svg" : CytobandToSvg.md

- "dict2bed" : DictToBed.md

- "evadumpfiles" : EVADumpFiles.md

- "fasta2vcf" : ReferenceToVCF.md

- "fastqgrep" : FastqGrep.md

- "fastqshuffle" : FastqShuffle.md

- "findallcoverageatposition" : FindAllCoverageAtPosition.md

- "findavariation" : FindAVariation.md

- "findgvcfsblocks" : FindGVCFsBlocks.md

- "findhtsfiledict" : FindHtsFileDictionary.md

- "fixvcfmissinggenotypes" : FixVcfMissingGenotypes.md

- "gatkhc" : GatkHaplotypeCaller.md

- "gff2kg" : Gff2KnownGene.md

- "gff3upstreamorf" : Gff3UpstreamOrf.md

- "goutils" : GoUtils.md

- "groupbygene" : GroupByGene.md

- "gtexrs2qtl" : GtexRsToQTL.md

- "gtf2bed" : GtfToBed.md

- "gtf2xml" : Gtf2Xml.md

- "gtfliftover" : GtfLiftOver.md

- "gtfretrocopy" : GtfRetroCopy.md

- "haplogroupcasectrl" : HaploGroupCaseControl.md

- "howmanybamdict" : HowManyBamDict.md

- "htsfreemarker" : HtsFreemarker.md

- "ibd2vcf" : IbdToVcf.md

- "illuminadir" : IlluminaDirectory.md

- "indexcov2vcf" : IndexCovToVcf.md

- "kg2bed" : KnownGenesToBed.md

- "kg2fa" : KnownGeneToFasta.md

- "kg2gff" : KgToGff.md

- "knowndel" : KnownDeletion.md

- "knownretrocopy" : KnownRetroCopy.md

- "liftover2svg" : LiftOverToSVG.md

- "lowresbam2raster" : LowResBam2Raster.md

- "manhattan" : Manhattan.md

- "mantamerger" : MantaMerger.md

- "mergeblastxml" : MergeBlastXml.md

- "mergesplittedblast" : MergeSplittedBlast.md

- "minicaller" : MiniCaller.md

- "mkminibam" : MakeMiniBam.md

- "msa2vcf" : MsaToVcf.md

- "multiqcpostproc" : MultiqcPostProcessor.md

- "ncbitaxonomy2xml" : NcbiTaxonomyToXml.md

- "ngsfilessummary" : NgsFilesSummary.md

- "oboutils" : OboUtils.md

- "optimizefisher" : OptimizeFisher.md

- "pcrclipreads" : PcrClipReads.md

- "pcrslicereads" : PcrSliceReads.md

- "plotbcftoolsstats" : PlotBcftoolsStats.md

- "plotmosdepth" : PlotMosdepth.md

- "plotsashimi" : PlotSashimi.md

- "prettysam" : PrettySam.md

- "pubmed404" : Pubmed404.md

- "pubmedauthorgraph" : PubmedAuthorGraph.md

- "pubmedcodinglang" : PubmedCodingLanguages.md

- "pubmeddump" : PubmedDump.md

- "pubmedgender" : PubmedGender.md

- "pubmedgraph" : PubmedGraph.md

- "pubmedmap" : PubmedMap.md

- "reduceblast" : ReduceBlast.md

- "ref2html" : ReferenceToHtml.md

- "repairfastq" : RepairFastq.md

- "sam2json" : SamToJson.md

- "sam2psl" : SamToPsl.md

- "sam2tsv" : Sam2Tsv.md

- "sam4weblogo" : SAM4WebLogo.md

- "samaddpi" : SamAddPI.md

- "samclipindelfraction" : SamClipIndelFraction.md

- "samedict" : SameDict.md

- "samextractclip" : SamExtractClip.md

- "samfindclippedregions" : SamFindClippedRegions.md

- "samfixcigar" : SamFixCigar.md

- "samgrep" : SamGrep.md

- "samjdk" : SamJdk.md

- "samrmdupnames" : SamRemoveDuplicatedNames.md

- "samviewwithmate" : SamViewWithMate.md

- "scanlabguru" : ScanLabGuru.md

- "scanretrocopy" : ScanRetroCopy.md

- "setfile2bed" : SetFileToBed.md

- "setfilecluster" : SetFileCluster.md

- "setfilefrombed" : SetFileFromBed.md

- "setfiletools" : SetFileTools.md

- "sortsamrefname" : SortSamRefName.md

- "sortvcfoninfo" : SortVcfOnInfo.md

- "splitvcf" : SplitVcf.md

- "starretrocopy" : StarRetroCopy.md

- "sv2fasta" : StructuralVariantToFasta.md

- "sv2svg" : SvToSVG.md

- "svcasescontrols" : SVCasesControls.md

- "swingbamcov" : SwingBamCov.md

- "swingbamview" : SwingBamView.md

- "swingindexcov" : SwingIndexCov.md

- "swingplinkselectcluster" : SwingPLinkSelectCluster.md

- "swingvcfjexl" : SwingVcfJexlFilter.md

- "swingvcfview" : SwingVcfView.md

- "texbam" : TextBam.md

- "tssenrich" : TSSEnrichment.md

- "ukbiobanksamples" : UKBiobankSelectSamples.md

- "uniprot2svg" : UniprotToSvg.md

- "variantsinwindow" : VariantsInWindow.md

- "vcf2bam" : VcfToBam.md

- "vcf2hilbert" : VcfToHilbert.md

- "vcf2intervals" : VcfToIntervals.md

- "vcf2r" : VcfToRScript.md

- "vcf2table" : VcfToTable.md

- "vcf2xml" : Vcf2Xml.md

- "vcfallelebalance" : VcfAlleleBalance.md

- "vcfancestralalleles" : VcfAncestralAllele.md

- "vcfbigbed" : VcfBigBed.md

- "vcfbigwig" : VCFBigWig.md

- "vcfbraiding" : VcfBraiding.md

- "vcfburdenfisherh" : VcfBurdenFisherH.md

- "vcfburdenmaf" : VcfBurdenMAF.md

- "vcfburdenslidingwindow" : VcfBurdenSlidingWindow.md

- "vcfcadd" : VcfCadd.md

- "vcfcombinetwosnvs" : VCFCombineTwoSnvs.md

- "vcfcomposite" : VCFComposite.md

- "vcfconcat" : VcfConcat.md

- "vcfdistancevariants" : VcfDistanceBetweenVariants.md

- "vcffilterbyliftover" : VcfFilterByLiftOver.md

- "vcffiltergenes" : VcFilterGenes.md

- "vcffiltergtf" : VcfFilterGtf.md

- "vcffilterjdk" : VcfFilterJdk.md

- "vcffilterso" : VcfFilterSequenceOntology.md

- "vcfflatten" : VCFFlatten.md

- "vcfgatkeval" : VcfGatkEval.md

- "vcfgenesplitter" : VcfGeneSplitter.md

- "vcfgnomad" : VcfGnomad.md

- "vcfgnomadsv" : VcfGnomadSV.md

- "vcfgrantham" : VcfGrantham.md

- "vcfgroupbypop" : VcfGroupByPopulation.md

- "vcfhead" : VcfHead.md

- "vcfmovefilterstoinfo" : VcfMoveFiltersToInfo.md

- "vcfmulti2one" : VcfMultiToOne.md

- "vcfmulti2oneallele" : VcfMultiToOneAllele.md

- "vcfmulti2oneinfo" : VcfMultiToOneInfo.md

- "vcfpar" : VcfPseudoAutosomalRegion.md

- "vcfpeekaf" : VcfPeekAf.md

- "vcfpeekvcf" : VcfPeekVcf.md

- "vcfphased01" : VcfPhased01.md

- "vcfpolyx" : VCFPolyX.md

- "vcfrebase" : VcfRebase.md

- "vcfregulomedb" : VcfRegulomeDB.md

- "vcfrenamechr" : ConvertVcfChromosomes.md

- "vcfscanupstreamorf" : VcfScanUpstreamOrf.md

- "vcfserver" : VcfServer.md

- "vcfsetdict" : VcfSetSequenceDictionary.md

- "vcfshuffle" : VCFShuffle.md

- "vcfspliceai" : VcfSpliceAI.md

- "vcfsplitnvariants" : VcfSplitNVariants.md

- "vcfspringfilter" : VcfSpringFilter.md

- "vcfstats" : VcfStats.md

- "vcfstrech2svg" : VcfStrechToSvg.md

- "vcfsvannotator" : VCFSVAnnotator.md

- "vcftabixml" : VCFTabixml.md

- "vcftail" : VcfTail.md

- "vcftbi2bed" : VcfTbiToBed.md

- "vcftrio" : VCFTrios.md

- "wescnvsvg" : WesCnvSvg.md

- "wgscoverageplotter" : WGSCoveragePlotter.md

- "wib2bedgraph" : WibToBedGraph.md

- "xcontaminations" : XContaminations.md

- "xsltstream" : XsltStream.md