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mkdocs.yml
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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
- "applyvelocity" : ApplyVelocity.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
- "biostar9608448" : Biostar9608448.md
- "blast2sam" : BlastToSam.md
- "blastfilterjs" : BlastFilterJS.md
- "blastmapannots" : BlastMapAnnotations.md
- "blastn2snp" : BlastNToSnp.md
- "breakdancer2vcf" : BreakdancerToVcf.md
- "builddbsnp" : BuildDbsnp.md
- "cmpbams" : CompareBams.md
- "cmpbams4" : CompareBams4.md
- "cmpbamsandbuild" : CompareBamAndBuild.md
- "cnvpanelofnormal" : CNVPaneOfNormal.md
- "cnvtview" : CnvTView.md
- "cnvvalidatorserver" : CNVValidatorServer.md
- "commbams" : CommBams.md
- "convertliftoverchain" : ConvertLiftOverChain.md
- "copynumber01" : CopyNumber01.md
- "coveragegrid" : CoverageGrid.md
- "coveragematrix" : CoverageMatrix.md
- "coverageplotter" : CoveragePlotter.md
- "coverageserver" : CoverageServer.md
- "cytoband2svg" : CytobandToSvg.md
- "dict2bed" : DictToBed.md
- "dict2r" : DictToR.md
- "dict2xml" : DictToXml.md
- "dragenbnd2inv" : DragenBndToInversion.md
- "evadumpfiles" : EVADumpFiles.md
- "extendrefwithreads" : ExtendReferenceWithReads.md
- "fasta2vcf" : ReferenceToVCF.md
- "fastqgrep" : FastqGrep.md
- "fastqrevcomp" : FastqRevComp.md
- "fastqshuffle" : FastqShuffle.md
- "findallcoverageatposition" : FindAllCoverageAtPosition.md
- "findavariation" : FindAVariation.md
- "findgvcfsblocks" : FindGVCFsBlocks.md
- "findhtsfiledict" : FindHtsFileDictionary.md
- "fixvcfmissinggenotypes" : FixVcfMissingGenotypes.md
- "gatkhc" : GatkHaplotypeCaller.md
- "gff2fasta" : Gff3ToFasta.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" : HtsVelocity.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
- "rnaseqpolya" : RNASeqPolyA.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
- "scansv" : ScanStructuralVariants.md
- "setfile2bed" : SetFileToBed.md
- "setfilecluster" : SetFileCluster.md
- "setfilefrombed" : SetFileFromBed.md
- "setfiletools" : SetFileTools.md
- "shiftbam" : ShiftBam.md
- "shiftvcf" : ShiftVcf.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
- "translategff3" : TranslateGff3.md
- "tssenrich" : TSSEnrichment.md
- "tview" : TViewCmd.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
- "vcfliftover" : VcfLiftOver.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
- "vcfstats2" : VcfStats2.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