Jvarkit : Java utilities for Bioinformatics


Tools

Name Description Keywords Terms Misc
samjsFilters a BAM using a javascript expression ( java nashorn engine ).sam bam nashorn javascript filter
casectrljfxchart of case/control maf from a VCF and a pedigreevcf pedigree case control visualization jfx chart maf
pubmedcodinglangProgramming language use distribution from recent programs / articlespubmed xml code programming
vcffixindelsFix samtools indels (for @SolenaLS)vcf indeluse `bcftools norm`.
vcftailprint the last variants of a vcfvcf
vcfheadprint the first variants of a vcfvcf
vcfmulti2oneallele'one variant with N ALT alleles' to 'N variants with one ALT'vcf
vcfinOnly prints variants that are contained/not contained into another VCFvcf compare
vcfpredictionsBasic Variant Effect prediction using ucsc-known genevcf annotation prediction
vcffiltersoFilter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user's SO-terms will be also used.<vcf filter sequenceontology prediction so
vcffilterjsFiltering VCF with javascript expressionsvcf filter javascript json nashorn
vcfpolyxNumber of repeated REF bases around POS.vcf repeat
vcfbedTransfer information from a BED to a VCFbed vcf annotation
vcftrioFind mendelian incompatibilitie / denovo variants in a VCFvcf mendelian pedigree denovo
groupbygeneGroup VCF data by gene/transcript. By default it uses data from VEP , SnpEffvcf gene
addlinearindextobedUse a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart.bed reference
almostsortedvcfSort an 'almost' sorted VCF. Most variants should be sorted but a few consecutive lines might have been switched by a caller.
backlocateMapping a mutation on a protein back to the genome.vcf annotation prediction protein
bam2fastqSame as picard/SamToFastq but allow missing reads + shuffle reads using hash(name) so you can use them with bwa. fastquse picard.
bam2rasterBAM to raster graphicsbam alignment graphics visualization png
bam2svgBAM to Scalar Vector Graphics (SVG)bam alignment graphics visualization svg
bam2xmlconverts a BAM to XMLsam bam xml
bam2wigBam to fixedStep Wiggle converter , or BED GRAPH. Parses the cigar String to get the depth. Memory intensive: must alloc sizeof(int)*size(chrom)bam wig wiggle bed
bamcmpcoverageCreates the figure of a comparative view of the depths sample vs sample. Memory consideration: the tool alloc an array of bits which size is: (MIN(maxdepth-mindepth,pixel_width_for_one_sample) * count_samples)^2sam bam visualization coverage
bamrenamechrConvert the names of the chromosomes in a BAM filesam bam chromosome contig
bamstats04Coverage statistics for a BED file.sam bam coverage depth statistics bed
bamstats05Coverage statistics for a BED file, group by genebam coverage statistics bed
batchigvpictures
bedliftoverLift-over a VCF filebed liftover
bedrenamechrConvert the names of the chromosomes in a Bed filebed chromosome contig convert
biostar103303Calculate Percent Spliced In (PSI).sam bam psi
biostar130456Split individual VCF files from multisamples VCF filevcf samples sample
biostar59647SAM/BAM to XMLsam bam xml
biostar76892fix strand of two paired reads close but on the same strand. sam bam
biostar77288Low resolution sequence alignment visualizationbam sam visualization svg alignment
biostar77828Divide the human genome among X cores, taking into account gapsworkflow reference parallel
biostar78285Extract BAMs coverage as a VCF file.sam bam depth coverage
biostar78400add the read group info to the sam file on a per lane basissam bam xml read-group
biostar81455Defining precisely the exonic genomic context based on a position .bed gene knownGene ucsc
biostar84452remove clipped bases from a BAM filesam bam clip
biostar84786Matrix transpositionmatrix util
biostar86363Set genotype of specific sample/genotype comb to unknown in multisample vcf file. See http://www.biostars.org/p/86363/sample genotype vcf
biostar86480Genomic restriction finderrebase genome enzyme restricion genome
biostar90204Bam version of linux split.sam bam split util
msa2vcfGetting a VCF file from a CLUSTAW or a FASTA alignment. vcf snp msa alignmentuse https://github.com/sanger-pathogens/snp_sites.
biostar95652Drawing a schematic genomic context tree.genbank svg tree evolution
biostar139647Convert alignment in Fasta/Clustal format to SAM/BAM filemsa sam bam clustal
biostar145820subsample/shuffle BAM to fixed number of alignments.sam bam shuffle
blastmapannotsMaps uniprot/genbank annotations on a blast result.blast annotation genbank uniprot
buildwpontologyBuild a simple RDFS/XML ontology from the Wikipedia Categorieswikipedia ontology rdf gui
bwamemdigest
bwamemnopMerge the other BWA-MEM alignements with its SA:Z:* attributes to an alignment containing a cigar string with 'N' ( Skipped region from the reference.)bwa sam bam
cmpbamsCompare two or more BAM filessam bam compare
cmpbamsandbuildCompare two BAM files mapped on two different builds. Requires a liftover chain file
coveragenormalizernormalize BAM coverage
downsamplevcfDownSample a VCF. Will keep 'n' random variants in a vcf.vcf
evs2vcfDownload data from EVS http://evs.gs.washington.edu/EVS as a BED chrom/start/end/XML For later use, see VCFTabixml.
evsdumpxmlDownload data from EVS http://evs.gs.washington.edu/EVS as XML file.
fastq2fastafastq -> fastafastq fastause awk, samtools....
kg2bedconverts UCSC knownGenes file to BED.ucsc bed knownGenes
fastqentropyCompute the Entropy of a Fastq file (distribution of the length(gzipped(sequence))fastq
fastqgrepGrep reads names in fastqfastquse picard.
fastqjsFilters a FASTQ file using javascript( java nashorn engine). fastq
fastqphred64to33Convert Illumina Fastq 64 encoding to Fastq 33fastq
fastqrevcompproduces a reverse-complement fastq (for mate pair alignment see http://seqanswers.com/forums/showthread.php?t=5085 )fastq
fastqshuffleShuffle Fastq filesfastq
fastqsplitinterleavedSplit interleaved Fastq files.fastq
findallcoverageatpositionFind depth at specific position in a list of BAM files. My colleague Estelle asked: in all the BAM we sequenced, can you give me the depth at a given position ?bam coverage search depth
findavariationFinds a specific mutation in a list of VCF filesvcf variation search
findcorruptedfilesReads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ/BED/TBI/BAI)vcf bam fastq bed
findmyvirusFind my Virus. Created for Adrien Inserm. Proportion of reads mapped on HOST/VIRUS.bam virus
findnewsplicesitesuse the 'N' operator in the cigar string to find unknown splice sitesrnaseq splice
fixvarscanmissingheader Fix the sample name in the #CHROM header and fix VCF header missingh in varscan2. Sometimes, but not always, it happends. See http://seqanswers.com/forums/showthread.php?t=33235
fixvcfFix a VCF if INFO or FILTER are missing
fixvcfformatFix PL format in VCF. Problem is described in http://gatkforums.broadinstitute.org/discussion/3453
fixvcfmissinggenotypesAfter a VCF-merge, read a VCF, look back at some BAMS to tells if the missing genotypes were homozygotes-ref or not-called. If the number of reads is greater than min.depth, then a missing genotype is said hom-ref.sam bam vcf sv genotype
gcpercentanddepthExtracts GC% and depth for multiple bam using a sliding windowgc% depth coverage
genomicjasparFind jaspar patterns in FASTA sequences. Reports a BED file.jaspar genomic pattern
howmanybamdictfinds if there's are some differences in the sequence dictionaries.sam bam dict
illuminadirCreate a structured (**JSON** or **XML**) representation of a directory containing some Illumina FASTQs.json xml illumina fastq workflow
ilmnfastqstatsReads filenames from stdin: Count FASTQs in Illumina Result.
impactofduplicatesImpact of Duplicates per BAM.bam
liftover2svgConvert LiftOver chain files to animated SVGsvg liftover ucsc xml
mapuniprotmap uniprot features on reference genomeuniprot bed fasta reference xjc xml
mergesplittedblastmerge blast Hits from splitted BLAST databaseblast
ncbitaxonomy2xmlDump NCBI taxonomy tree as a hierarchical XML documenttaxonomy ncbi xml
samjmxMonitor/interrupt/break a BAM/SAM stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.htmlsam bam jmx monitoring
ngsfilessummaryScan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). Useful to get a summary of your samples.sam bam vcf util
noemptyvcfIf VCF is empty or doesn't exists, create a dummy oneWas developped at the time where VEP didn't send an output if there was no variant, just a header in the source vcf..
nozerovariationvcfcat a whole VCF, or, if there is no variant, creates a fake onevcf
pademptyfastqPad empty fastq sequence/qual with N/#fastquse awk.
pubmeddumpDump XML results from pubmed/Eutilsncbi pubmed xml
pubmedorcidgraphCreates a graph from Pubmed and Authors' Orcid identifierspubmed ncbi orcid
pubmedfilterjsFilters Pubmed XML with a javascript (java rhino) expression. Context contain 'article' a PubmedBookArticle or a PubmedArticle and 'index', the index in the XML file.pubmed javascript xml ncbi
referencetovcfCreates a VCF containing all the possible substitutions from a Reference Genome.vcf reference fasta
sam2jsonConvert a SAM input to JSONsam bam json
sam2pslConvert SAM/BAM to PSL http://genome.ucsc.edu/FAQ/FAQformat.html#format2 or BED12sam bam psluse bedtools/bamtobed.
sam2tsvPrints the SAM alignments as a TAB delimited file.sam bam table tsv
SamclipindelfractionExtract clipping/indel fraction from BAMsam bam clipThis tool can be replace with Bioalcidaejdk.
samextractclipExtract Soft Clipped Sequences from a SAM. Ouput is a FASTQsam bam fastq clip
samfixcigarFix Cigar String in SAM replacing 'M' by 'X' or '='sam bam cigar
samgrepgrep read-names in a bam filesam bam
samshortinvertScan short inversions in SAMsam bam sv inversion
samstats01Statistics about the reads in a BAM.
sortvcfoninfoSort a VCF a field in the INFO columnvcf sort annotation
sortvcfonref2Sort a VCF using the internal dictionary or an external reference order (Deprecated: use picard SortVcf).vcf sortuse picard sortvcf.
splitbytileSplit Bam By tilesam bam
vcf2hilbertPlot a Hilbert Curve from a VCF file.vcf image visualization
vcf2postscriptPrint VCF context as Postscriptvcf postscript
vcf2rdfconvert VCF to RDF (N3 notation)vcf rdf
vcf2sqlGenerate the SQL code to insert a VCF into mysqlvcf sql
vcf2xmlConvert VCF to XMLvcf xml
vcfbiomartBiomartQueries with VCFvcf ensembl biomart annotation
vcfcaddAnnotate VCF with Combined Annotation Dependent Depletion (CADD) (Kircher & al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.PubMed PMID: 24487276.vcf prediction cadd annotation
vcfcmppredCompare predictions (SNPEff, VEP) for several VCFs
vcfcommEquivalent of linux comm for VCF
vcfcompareCompares two VCF filesvcf compare
vcfcomparegt compare two or more genotype-callers for the same individuals. Produce a VCF with FORMAT fields indicating if a genotype is new or modified.vcf compare
vcfconcatConcatenante sorted VCF with same sample, does NOT merge genotypesvcf
vcfcutsamplesSelect/Exclude some samples from a VCFvcf sampleuse bcftools or gatk SelectVariants.
vcfjasparFinds JASPAR profiles in VCFvcf matrix jaspar
vcfliftoverLift-over a VCF filevcf liftover
vcfmergeMerge VCF Filesvcf sortuse GATK combineVariants..
vcfmulti2one>Convert VCF with multiple samples to a VCF with one SAMPLE, duplicating variant and adding the sample name in the INFO columnvcf sample
vcfregulomedbAnnotate a VCF with the Regulome data (http://regulome.stanford.edu/
vcfrenamechrConvert the names of the chromosomes in a VCF filevcf contig chromosome convertuse `bcftools annotate` with `--rename-chrs file`.
vcfrenamesamplesRename the Samples in a VCFvcf sample
vcfresetvcfReset Genotypes in VCF (./.) if they've been found in another VCF indexed with tabixvcf genotype
vcfsetdictSet the `##contig` lines in a VCF header on the flyvcf dict fai
vcfshuffleShuffle a VCFvcf
vcfSimulatorGenerate a VCFvcf
vcfstatsProduce VCF statiticsvcf stats burden gnuplot
vcfcombinetwosnvsDetect Mutations than are the consequences of two distinct variants. This kind of variant might be ignored/skipped from classical variant consequence predictor. Idea from @SolenaLS and then @AntoineRimbertvcf annotation prediction protein mnv
vcfstripannotRemoves one or more field from the INFO/FORMAT column of a VCF.vcfUse bcftools annotate -x .
vcftabixml annotate a value from a vcf+xml filevcf xml
vcfvcfGet the INFO from a VCF and use it for another VCFobsolete. use GATK.
worldmapgenomeGenome/Map of the world. Input is a BED file: chrom/start/end/country.gis
uniprotfilterjsFilters Uniprot DUMP+ XML with a javascript (java rhino) expression. Context contain 'entry' an uniprot entry and 'index', the index in the XML file.unitprot javascript xjc xml
skipxmlelementsFilter XML elements with a javascript (java rhino) expression. Context contain 'element' the current element. It implementsthe interface Tag described in SkipXmlElements.classxml javascript
vcfensemblvepAnnotate a VCF with ensembl REST APIvcf annotation rest ensembl xml xslt xsl
vcfgroupbypopGroup VCF data by population, creates a VCF where each 'SAMPLE' is a population
bamtileAnswer to @sjackman : Is there a bedtools command to determine a minimal tiling path? A minimal set of features that cover a maximum of the target.bam sam
xcontaminationsFor @AdrienLeger2 : cross contamination between samples by looking at the homozygous genotypes.sam bam vcf contamination
biostar3654show blast alignment with annotationsblast xml annotation
vcfburdenSolena: vcf to (chrom/pos/ref/alt/individus(G:0/1/2/-9)deprecated.
vcfreplacetagReplace the key for INFO/FORMAT/FILTERvcfuse `bcftools annotate` with option `-c`.
vcfpeekvcfGet the INFO from a VCF and use it for another VCFvcf annotation
vcfgetvariantbyIndexAccess a Plain or BGZF-compressed VCF file by indexvcf
vcfmulti2oneinfo'one INFO with N values' to 'N variants with one INFO'vcf
bedindextabixIndex and sort a Bed on the fly with Tabix.bed tabix
vcf2bamvcf to bamref vcf bam
vcffilterxpathFilter a VCF with a XPATH expression on a INFO tag containing a base64 encodede xml documentvcf xml xpath
biostar140111How to obtain human genotype data from dpSNP ftp?
extendrefwithreadsExtending ends of sequences with the help of readsread fastq reference sam bam
pcrslicereadsMark PCR reads to their PCR ampliconpcr sam bam cigar
vcfjmxMonitor/interrupt/break a VCF stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.htmljava jmx vcf
gtf2xmlConvert GTF/GFF to XMLxml gtf gff gff3
sortsamrefnameSort a BAM of contig and then on namesam sort
biostar154220Cap BAM to a given coveragebam sam coverage
biostar160470Getting untranslated nucleotide sequences on tblastn standalone blasn blast translation protein
biostar165777Split a XML filexml
vcfcomparecallersCompare two VCFs and print common/exclusive information for each sample/genotypevcf compare genotype
bamclip2insertionConvert SOFT clip to Insertion of other read confirm itsam bam clip
biostar170742convert sam format to axt Formatsam axt
biostar172515Convert BAI to XMLbai bam xml
biostar173114make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114/sam bam
biostar175929Construct a combination set of fasta sequences from a vcffasta vcf
vcfcalledwithanothermethodCompare one vcf with other , add a flag to tell if a variant was called with another method. Vcf must be sorted on the same Dict.vcf compare concordance
biostar178713split bed file into several bed files where each region is separated of any other by N basesbed
vcfremovegenotypejsReset Genotype in VCF using a javascript expression
bamstats02Statistics about the flags and reads in a BAM
bamstats02viewStatistics about the flags and reads in a BAM. Visualize date from BamStats02
biostar105754bigwig : peak distance from specific genomic regionwig bigwig
bam2sqlConvert a SAM/BAM to sqlite statementsbam sam sql sqlite
vcf2zipReads a stream of concatenated VCFs and insert them into a Zip file
pubmedgenderAdd gender-related attributes in the Author tag of pubmed xml. pubmed gender ncbi xml
pubmedmapUse Pubmed Author's Affiliation to map the authors in the world.pubmed xml gis map
splitvcfsplit a vcf using a named list of intervals...vcf
forkvcfFork a VCF.
bim2vcfconvert a .bim to a .vcf . For @FlorianeS44bim vcf
concatsamconcat sam filessam bam
samreadlengthdistributionSam read length distributionsam bam histogram
biostar214299Extract allele specific reads from bamfilessam bam variant snp
cmpbams4Compare two BAM files. Print a tab-delimited reportsam bam compare
biostar234081convert extended CIGAR to regular CIGAR ('X','=' -> 'M')sam bam cigar
vcfgnomadPeek annotations from gnomadvcf annotation gnomad
vcf2svgwrite a vcf to svg , with gene contextvcf svg xlm visualization
mergeblastxmlmerge XML blast results (same Iteration/Iteration_query-def in multiple xml filesblast xml
vcfannotwithbeaconAnnotate a VCF with ga4gh beaconga4gh beacon vcf annotation
commbamsEquivalent of unix 'comm' for bams sorted on querynamesam bam comm compare
samscansplitreadsscan split readssam sv splitreads clip
samretrieveseqandqualI have a query-sorted BAM file without read/qual sequences and a FASTQ file with the read/qual sequences. Is there a tool to add seq to BAM? for @sjackman https://twitter.com/sjackman/status/575368165531611136
biostar234230Sliding Window : discriminate partial and fully contained fragments (from a bam file)
biostar251649 Annotating the flanking bases of SNPs in a VCF filevcf annotation sequence reference
vcfbedsetfilterSet FILTER for VCF if intersects with BED.vcf bed filter
bamliftoverLift-over a BAM file.bam liftover
blast2samConvert a **BLASTN-XML** input to SAMsam blast
reduceblastReduce the size of XML blast, by removing iterations that have no Hitblast xml
blastn2snpprint indel/mismatch in a blastn streamblast snp
splitbam3Split a BAM by chromosome group
vcfindextabixIndex and sort a VCF on the fly with Tabixvcf tabix
blastfilterjsFilters a BlastOutput with a javascript expression. The script injects each <Hit> as the variable 'blasthit'. The user script should return 'true' to keep the hit.blast js javascript filter
SamSlopextends sam by 'x' bases
vcfgenesplitterSplit VCF+VEP by gene/transcript.genes vcf
sammaskalignedbasesMask bases aligned on Reference.
queue2makeConvert Broad/Queue genomestrip Log stream to Makefile.
pcrclipreadsSoft clip bam files based on PCR target regionssam bam pcr bed
vcfeigenAnnotator for the data of https://xioniti01.u.hpc.mssm.edu/v1.1/ : Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as made available by the ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance.vcf annotation variant
vcfmovefilterstoinfoMove any FILTER to the INFO column. reset FILTER to PASSvcf burden format info
vcfburdenmafBurden : MAF for Cases / Controls vcf burden maf case control
vcfburdenfisherhFisher Case /Controls per Variantvcf burden fisher
vcfinjectpedigreeInjects a pedigree (.ped) file in the VCF headervcf pedigree burden
samcolortagAdd the UCSC 'YC' color tag in a BAM. See http://software.broadinstitute.org/software/igv/book/export/html/6 and http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.htmlsam bam metadata javascript igv visualization
vcffilternotinpedigreeAdds a FILTER 'NotInPedigree' if the only not(homref) genotypes are not in a pedigreeburden vcf pedigree
vcfburdenexacBurden filter 3 - Exacvcf burden exac
vcf2tableconvert a vcf to a table, to ease display in the terminalvcf table visualization
vcfburdenfiltergenesFilter VEP/SnpEff Output from a list of genes.gene vcf vep snpeff
vcfrefbaseRestriction sites overlaping variations in a vcfvcf rebase restriction enzyme
projectserverJetty Based http server serving VCF, BAM files
allelefreqcalcAllele Frequency Calculatorvcf afUse bioalcidae.
bamindexreadnamesBuild a dictionary of read names to be searched with BamQueryReadNames
bamtreepackCreate a TreeMap from one or more SAM/BAM file. Ouput is a SVG file.bam treepack
fastqrecordtreepackCreate a TreeMap from one or more Fastq file. Ouput is a SVG file
samfindclippedregionsFins clipped position in one or more bam. Output is a VCF filesam bam clip vcf
vcftreepackCreate a TreeMap from one or more VCF. Ouput is a SVG file.
vcfburdensplitterSplit VCF Using a Burden Splitter (by gene, transcript, etc..)
vcfburdenfishervFisher Case / Controls per Variant (Vertical)vcf burden fisher
vcfburdenrscriptvFisher Case / Controls per Variant (Vertical)vcf burden fisher
vcfderby01Insert similar VCFs into an Apache Derby Databasevcf sql derby burden
vcfdoestgenerate Transcript information for DOEST testvcf burden doest
bioalcidaejavascript version of awk for bioinformaticssam bam vcf javascript js nashorn
picardmetrics2xmltransforms a picard metrics file to XML. See http://plindenbaum.blogspot.fr/2013/02/making-use-of-picard-metrics-files.htmlpicard xml metrics
casectrlcanvasdraw a chart of case/control maf from a stream of X/Y valuesvcf case control visualization jfx chart maf
lowresbam2rasterLow Resolution BAM to raster graphicsbam alignment graphics visualization png knowngene
Query a Bam file indexed with BamIndexReadNames
knime2txtconverts a Knime Workflow to a html representation.knime workflow convert
lumpyvcf2circosLumpy to Circoslumpy circos sv vcf
genscanPaint a Genome Scan picture from a Tab delimited file (CHROM/POS/VALUE1/VALUE2/....).chromosome reference chart visualization
vcfucscannotate an VCF with mysql UCSC dataucsc mysql vcf
xsltstreamXSLT transformation for large XML files. xslt is only applied on a given subset of nodes.xml xslt xsl stylesheet
vcfloopovergenesGenerates a BED file of the Genes in an annotated VCF, loop over those genes and generate a VCF for each gene, then execute an optional command.vcf gene burden
vcffilterjdkFiltering VCF with dynamically-compiled java expressionsvcf filter java jdk
optimizerGenetic-Programming-like parameters optimizergenetic-programming
bioalcidaejdkjava-based version of awk for bioinformaticssam bam vcf java jdk gtf
copynumber01experimental CNV detection. Doesn't work for now.cnv bam sam
samjdkFilters a BAM using a java expression compiled in memory.sam bam java jdk filter
vcfmakedictCreate a SAM Sequence Dictionary from a set of VCF files.vcf dict fai
vcfbigwigAnnotate a VCF with values from a bigwig filevcf wig wiggle bigwig
vcfnocall2homrefConvert the UNCALLED gentoypes in a VCF to HOM_REF. This tool can be used after using GATK CombineVariants.vcf
gff2kgConvert GFF3/GTF format to UCSC knownGene format.gff ,gtf knownGene ucsc convert
minicallerSimple and Stupid Variant Caller designed for @AdrienLeger2bam sam calling vcf
vcfoptimizeped4skatOptimize ped file for SKATvcf pedigree skat burden
vcfskatslidingwindowSkatFactory Over genome using a sliding window.vcf pedigree skat burden
vcfskatCalculate SKAT score for a VCF.vcf pedigree skat burden
vcfserverWeb Server displaying VCF file. A web interface for vcf2tablevcf table visualization server web
tviewserverWeb Server displaying SAM/BAM file. A web interface for jvarkit:tviewsam bam table visualization server web
pubmedgraphCreates a Gephi-gexf graph of references-cites for a given PMIDpubmed xml graph
vcftrapannotate vcf with trap database http://trap-score.org/vcf trap annotation
trapindexerConvert text data to binary format for the trap DATABASE database http://trap-score.org/. Those data can be used by the tool `vcftrap`.trap
prettysamPretty SAM alignmentssam bam
vcfremoveunusedaltRemove unused ALT allele if there is no genotype with this alt, or there is no sample but AC=0vcf genotype
variantsinwindowAnnotate Number of Variants overlaping a sliding window.vcf annotation
samaddpiAdd predicted median insert size 'PI' to SAM Read groups (RG).sam bam
goutilsGene Ontology Utils. Retrieves terms from Gene Ontologygeneontology go gexf
gb2gffExperimental genbank to GFFxml ncbi genbank convert gff gb
indexcovjfxdisplay indexcov data in a jfx clientcnv jfx duplication deletion sv
indexcov2vcfconvert indexcov data to vcfcnv jfx duplication deletion sv
tviewequivalent of samtools tviewsam bam visualization terminal
samcustomsortjdkSort a BAM file using a java expression compiled at runtime.sam bam java jdk sort
simpleplotsimple figure plotter output is a R scriptchar figure
cytoband2svgCreates a svg karyotype .karyotype svg ideogram
vcfstatsjfxVCF statisticsvcf stats
vcfancestralallelesAnnotate a VCF with it's ancestral allele. Data from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.READMEvcf sort
vcfgoFind the GO terms for VCF annotated with SNPEFF or VEPvcf godo not use this.
vcfcomparecallersonesampleFor my colleague Julien: VCF with one sample called using different callers. Only keep variant if it was found in min<x=other-files<=maxvcf compare
bednonoverlappingsetSplit a Bed file into non-overlapping data set.bed
vcfafinfofilterFilter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomadvcf annotation gnomad
biostar322664Extract PE Reads (with their mates) supporting variants in vcf filesam bam vcf
vcfcomposite(in developpement) Finds Variants involved in a Het Compound Diseasevcf disease annotation pedigree haplotype
biostar92368Binary interactions depth.protein interaction interactome
wescnvsvgSVG visualization of bam DEPTH for multiple regionsbam alignment graphics visualization svg wes bed capture exome
naivecnvdetectorexperimental CNV detection for multiple samples.cnv bam sam wig bigwig bigbed
vcfclusteredreadedgeVariant annotation : variants clustered near the ends of readssam bam vcf
biostar332826Fast Extraction of Variants from a list of IDsvcf rs
pubmedauthorgraphCreates a graph from Pubmed and Authorspubmed ncbi graph
gephicmdCmd-line oriented for gephi.graph gexf gephi visualization
gexftrGexf file manipulationgexf graph network
ncbigenedumpDump XML results from a list of gene using NCBI/Eutilsncbi gene xml
vcfallelebalanceInsert missing allele balance annotation using FORMAT:ADvcf allele-balance depth
vcfgapfrequentFilter VCF annotated with external (AF or AC/AN) frequency information like vcfgnomadvcf
biostar336589displays circular map as SVG from BED and REF filegenome browser circular bed svg
bamslicebedFor @wouter_decoster : slice (long reads) overlapping the records of a BED filesam bam bed
mergecnvnatorMerge CNVNator resultscnv indel cnvnator
faidxsplitterSplit bed of reference genome into overlapping partsvcf reference bed
wescnvtviewSVG visualization of bam DEPTH for multiple regions in a terminalbam alignment graphics visualization svg cnv
sv2svgBAM to SVG. Used to display the structural variations.bam alignment graphics visualization svg
vcf2bedvcf to bedbed vcf
biostar352930Fills the empty SEQ(*) and QUAL(*) in a bam file using the the reads with the same name carrying this information.sam bam
pubmed404Test if URL in the pubmed abstracts are reacheable.pubmed url
vcfstrechofgtTry to finds deletion by searching strech of HOM_REF/HOM_VAR/NO_CALL Genotypes.vcf deletion
haloplexparasitefor @SolenaLS : remove artctifacts from haloplex that gives indels in GATK hapcaller vcf haloplex
ngsfilesscannerBuild a persistent database of NGS file. Dump as XML.ngs bam sam vcf xml
vcfburdensplitter2new versionvcf burden gene vep snpeff prediction
vcfensemblregAnnotate a VCF with the UCSC genome hub tracks for Ensembl Regulation.vcf ensembl regulation
scanretrocopyScan BAM for retrocopiessam bam cigar clip sv retrocopy
sigframeSigFrame displays CGH/ position+values in a GUIcgh gui visualization
samviewwithmateExtract reads within given region(s), and their matessam bam
kg2faconvert knownGenes to fastakg knownGene fasta
vcfscanupstreamorfScan BAM for upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs vcf uorf
vcfgnomadpextPeek annotations from gnomadpextvcf annotation gnomad
vcfsparqlQuery RDF with Sparql. Very slow. Just a proof of conceptvcf sparql rdf arq semanticweb
samtranslocationsExplore balanced translocations between two chromosomes using discordant paired-end reads.sam bam sv translocation
convertliftoverchainConvert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...)chain liftover
mkminibamCreates an archive of small bams with only a few regions.bam sam
vcfdistancevariantsAnnotate variants with the distance between previous and next variant.vcf annotation distance
hicfileinfoPrints information about a HI-C File/URLhic
vcfwindowsplitterSplit VCF by sliding windowvcf sliding window
bammatrixBam matrix, inspired from 10x/loupe sam bam compare matrix
vcfphased01X10 Phased SVG to Scalar Vector Graphics (SVG)x10 phased genotypes svg
starretrocopyScan retrocopies from the star-aligner/bwa outputsam bam cigar clip sv retrocopy star
ijgv2vcfConvert zips of Integrative Japanese Genome Variation to VCF file.vcf jgvd japan tommo
vcfadfractionfilter VCF for strange FORMAT:AD fractionvcf allele-balance depth
gtfsplitterSplit GTF file per gene, transcript, chromosome...gtf
gtfretrocopyScan retrocopies by comparing the gtf/intron and the deletions in a VCFgtf retrocopy deletion
vcfgnomadsvPeek annotations from gnomad structural variantsvcf annotation gnomad sv
knownretrocopyAnnotate VCF structural variants that could be intron from retrocopies.gtf retrocopy deletion
svpredictionsBasic Variant Effect prediction using gtfvcf annotation prediction sv
gtfliftoverLiftOver GTF file.gtf liftover
scansvScan structural variants for case/controls datacnv indel sv pedigree
bamheteroplasmyCall a VCF for the Mitochondria (Experimental)vcf sam bam mitochondria
findhtsfiledictScan a set of HTS files (VCF, BAM, CRAM), return a tab delimited file (path-of-file,path-to-fasta)sam bam cram vcf dict
biostar398854Extract every CDS sequences from a VCF filevcf gtf
psl2bamConvert PSL to SAM/BAMblat sam bam psl pslx
mantamergerMerge Vcf from Manta VCF.sv burden manta vcf
vcfburdenslidingwindowRun Burden Sliding windowvcf burden case control
depthofcoverageA custom 'Depth of Coverage'.depth bam sam coverage

Other Pages

Name Description Keywords Terms Misc
Knime IntegrationHow to use HTSJDK/Jvarkit in knimebam sam knime vcf annotation