JVARKIT
Author : Pierre Lindenbaum Phd. Institut du Thorax. Nantes. France. Version : 8ebd2be2 Compilation : 20240424122145 Github : https://github.com/lindenb/jvarkit Issues : https://github.com/lindenb/jvarkit/issues
Usage
java -jar jvarkit.jar [options]
or
java -jar jvarkit.jar <command name> (other arguments)
Options
- --help show this screen
- --help-all show all commands, including the private ones.
- --version print version
Compilation Installation
Please, read how to run and install jvarkit
Tools
BAM Visualization
| Tool | Description | Creation | Update |
|---|---|---|---|
| bam2raster | BAM to raster graphics | ||
| bam2svg | BAM to Scalar Vector Graphics (SVG) | 20141013 | 20210728 |
| biostar139647 | Convert alignment in Fasta/Clustal format to SAM/BAM file | ||
| biostar145820 | subsample/shuffle BAM to fixed number of alignments. | 20150615 | 20211005 |
| lowresbam2raster | Low Resolution BAM to raster graphics | 20170523 | 20211126 |
| mkminibam | Creates an archive of small bams with only a few regions. | 20190410 | 20221019 |
| plotsashimi | Print Sashimi plots from Bam | 20191117 | 20191104 |
| prettysam | Pretty SAM alignments | 20171215 | 20211105 |
| sv2svg | BAM to SVG. Used to display structural variations. | 20181115 | 20230505 |
| wgscoverageplotter | Whole genome coverage plotter | 20201125 | 20230505 |
CNV/SV
| Tool | Description | Creation | Update |
|---|---|---|---|
| bammatrix | Bam matrix, inspired from 10x/loupe | 20190620 | 20211206 |
| cnvtview | Text visualization of bam DEPTH for multiple regions in a terminal | 20181018 | 20210412 |
| coverageplotter | Display an image of depth to display any anomaly an intervals+bams | 20200605 | 20221125 |
| indexcov2vcf | convert indexcov data to vcf | 20200528 | 20400313 |
| samfindclippedregions | Fins clipped position in one or more bam. | 20140228 | 20220329 |
| swingindexcov | indexcov visualization | 2020511 | 2020512 |
| vcfstrech2svg | another VCF to SVG | 20210304 | 20210309 |
| wescnvsvg | SVG visualization of bam DEPTH for multiple regions | 20180726 | 20210726 |
Functional prediction
| Tool | Description | Creation | Update |
|---|---|---|---|
| backlocate | Mapping a mutation on a protein back to the genome. | 20140619 | 20190820 |
| groupbygene | Group VCF data by gene/transcript. By default it uses data from VEP , SnpEff | 20131209 | 20220529 |
BED Manipulation
| Tool | Description | Creation | Update |
|---|---|---|---|
| bedcluster | Clusters a BED file into a set of BED files. | 20200130 | 20220914 |
| bedmergecnv | Merge continuous sorted bed records if they overlap a fraction of their lengths. | 20200330 | 20200603 |
| bednonoverlappingset | Split a Bed file into non-overlapping data set. | 20180607 | 20200408 |
| bedrenamechr | Convert the names of the chromosomes in a Bed file | 20190503 | |
| setfiletools | Utilities for the setfile format | 20210125 | 20220426 |
Biostars
| Tool | Description | Creation | Update |
|---|---|---|---|
| biostar103303 | Calculate Percent Spliced In (PSI). | ||
| biostar105754 | bigwig : peak distance from specific genomic region | 20140708 | 20220110 |
| biostar165777 | Split a XML file | 20151114 | 20151114 |
| biostar170742 | convert sam format to axt Format | 20151228 | 20210412 |
| biostar172515 | Convert BAI to XML | ||
| biostar173114 | make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114/ | ||
| biostar175929 | Construct a combination set of fasta sequences from a vcf | 20160208 | 20211012 |
| biostar178713 | split bed file into several bed files where each region is separated of any other by N bases | 20160226 | 20200818 |
| biostar214299 | Extract allele specific reads from bamfiles | 20160930 | 20220420 |
| biostar234081 | convert extended CIGAR to regular CIGAR ('X','=' -> 'M') | 20170130 | 20200409 |
| biostar234230 | Sliding Window : discriminate partial and fully contained fragments (from a bam file) | 20190417 | |
| biostar251649 | Annotating the flanking bases of SNPs in a VCF file | 20170508 | 20200213 |
| biostar322664 | Extract PE Reads (with their mates) supporting variants in vcf file | ||
| biostar332826 | Fast Extraction of Variants from a list of IDs | 20180817 | 20210412 |
| biostar336589 | displays circular map as SVG from BED and REF file | 20180907 | 20210818 |
| biostar352930 | Fills the empty SEQ() and QUAL() in a bam file using the the reads with the same name carrying this information. | ||
| biostar398854 | Extract every CDS sequences from a VCF file | 20190916 | 20240418 |
| biostar404363 | introduce artificial mutation SNV in bam | 20191023 | 20191024 |
| biostar480685 | paired-end bam clip bases outside insert range | 20201223 | 20200220 |
| biostar489074 | call variants for every paired overlaping read | 20200205 | 20210412 |
| biostar497922 | Split VCF into separate VCFs by SNP count | 20210319 | 20210319 |
| biostar59647 | SAM/BAM to XML | 20131112 | 20190926 |
| biostar76892 | fix strand of two paired reads close but on the same strand. | ||
| biostar77288 | Low resolution sequence alignment visualization | ||
| biostar77828 | Divide the human genome among X cores, taking into account gaps | ||
| biostar78285 | Extract BAMs coverage as a VCF file. | ||
| biostar81455 | Defining precisely the exonic genomic context based on a position . | 20130918 | 20200603 |
| biostar84452 | remove clipped bases from a BAM file | ||
| biostar84786 | Matrix transposition | ||
| biostar86363 | Set genotype of specific sample/genotype comb to unknown in multisample vcf file. See http://www.biostars.org/p/86363/ | ||
| biostar86480 | Genomic restriction finder | 20131114 | 20220426 |
| biostar90204 | Bam version of linux split. | ||
| biostar9462889 | Extracting reads from a regular expression in a bam file | 20210402 | 20210402 |
| biostar9469733 | Extract reads mapped within chosen intronic region from BAM file | 20210511 | 20210511 |
| biostar9501110 | Keep reads including/excluding variants from VCF | 20211210 | 20211213 |
| biostar9556602 | Filtering of tricky overlapping sites in VCF |
Deprecated/barely used
| Tool | Description | Creation | Update |
|---|---|---|---|
| addlinearindextobed | Use a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart. | 20140201 | 20230126 |
| bam2sql | Convert a SAM/BAM to sqlite statements | 20160414 | 20160414 |
| bam2xml | converts a BAM to XML | 20130506 | 20210315 |
Pubmed
| Tool | Description | Creation | Update |
|---|---|---|---|
| pubmed404 | Test if URL in the pubmed abstracts are reacheable. | 20181210 | 20200204 |
| pubmedcodinglang | Programming language use distribution from recent programs / articles | 20170404 | 20200223 |
| pubmeddump | Dump XML results from pubmed/Eutils | 20140805 | 20200204 |
| pubmedgender | Add gender-related attributes in the Author tag of pubmed xml. | ||
| pubmedgraph | Creates a Gephi-gexf graph of references-cites for a given PMID | 20150605 | 20200220 |
GTF/GFF Manipulation
| Tool | Description | Creation | Update |
|---|---|---|---|
| gtf2bed | Convert GTF/GFF3 to BED. | 20220629 | 20220630 |
| gtf2xml | Convert GTF/GFF to XML | 20150811 | 20230512 |
Utilities
| Tool | Description | Creation | Update |
|---|---|---|---|
| goutils | Gene Ontology Utils. Retrieves terms from Gene Ontology | 20180130 | 20211020 |
| ncbitaxonomy2xml | Dump NCBI taxonomy tree as a hierarchical XML document or as a table | 20120320 | 20240320 |
| oboutils | OBO Ontology Utils. | 20230105 | 20230105 |
| ukbiobanksamples | Select samples from ukbiobank | 20210705 | 20220322 |
| uniprot2svg | plot uniprot to SVG | 20220608 | 20220922 |
| xsltstream | XSLT transformation for large XML files. xslt is only applied on a given subset of nodes. | 20190222 |
Unclassfied
| Tool | Description | Creation | Update |
|---|---|---|---|
| bamliftover | Lift-over a BAM file. | ||
| barcodegenerator | Barcode generator for EricCharp | 20230629 | 20230629 |
| bedremovebed | Remove bed file from each record of input bed file. Output is a SETFILE | 20221210 | 20221210 |
| bigwigmerge | merge several Bigwig files using different descriptive statistics (mean, median, etc..) | 20240417 | 20240417 |
| cnvvalidatorserver | Review files generated by coverageplotter | 20220818 | 20220826 |
| convertliftoverchain | Convert the contigs in a liftover chain to match another REFerence. (eg. to remove chr prefix, unknown chromosomes etc...) | 20190409 | 20190409 |
| coverageserver | Jetty Based http server serving Bam coverage. | 20200212 | 20200330 |
| evadumpfiles | Dump files locations from European Variation Archive | 20230314 | 20230314 |
| fastqshuffle | Shuffle Fastq files | 20140901 | 20240129 |
| gff3upstreamorf | Takes a ucsc genpred file, scan the 5' UTRs and generate a GFF3 containing upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs | 20220724 | 20230820 |
| gtexrs2qtl | extract gtex eqtl data from a list of RS | 20230215 | 20240225 |
| gtfliftover | LiftOver GTF file. | 20190823 | 20190823 |
| gtfretrocopy | Scan retrocopies by comparing the gtf/intron and the deletions in a VCF | 20190813 | 20191104 |
| htsfreemarker | Apply Freemarker to VCF/BAM/JSON files. | 20230616 | 20230616 |
| illuminadir | Create a structured (JSON or XML) representation of a directory containing some Illumina FASTQs. | 20131021 | 20180717 |
| kg2bed | converts UCSC knownGenes file to BED. | 20140311 | 20230815 |
| kg2fa | convert ucsc genpred to fasta | 20190213 | 20230815 |
| kg2gff | Convert UCSC genpred file to gff3 | 20210106 | 20230817 |
| knownretrocopy | Annotate VCF structural variants that could be intron from retrocopies. | 20190815 | 20230817 |
| ngsfilessummary | Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..). Useful to get a summary of your samples. | 20140430 | 20240324 |
| optimizefisher | Optimize fisher test on VCF using genetic algo | 20221013 | 20240207 |
| pubmedmap | Use Pubmed Author's Affiliation to map the authors in the world. | 20160426 | |
| repairfastq | Join single end reads to paired end | 20240128 | 20240128 |
| sam2json | Convert a SAM input to JSON | 20210402 | 20210315 |
| sam4weblogo | Sequence logo for different alleles or generated from SAM/BAM | 20130524 | 20191014 |
| samjdk | Filters a BAM using a java expression compiled in memory. | 20170807 | 20191119 |
| scanlabguru | scan the files stored in labguru | 20240325 | 20240325 |
| sortvcfoninfo | Sort a VCF a field in the INFO column | 20140218 | 20201204 |
| sv2fasta | convert VCF of structural variant(s) to fasta for pggb | 20230403 | 20230403 |
| tssenrich | Transcription Start Site (TSS) Enrichment Score calculation | 20240130 | 20240206 |
| vcf2bam | vcf to bam | 20150612 | 20211022 |
| vcf2xml | Convert VCF to XML | 20230822 | |
| vcfburdenfisherh | Fisher Case /Controls per Variant | 20160418 | 20200713 |
| vcfburdenslidingwindow | apply fisher test on VCF using a sliding window | 20190920 | 20231213 |
| vcffilterbyliftover | Add FILTER(s) to a variant when it is known to map elsewhere after liftover. | 20190418 | 20210603 |
| vcfgatkeval | Eval/Plot gatk INFO tags for filtering | 20230424 | 20240321 |
| vcfgroupbypop | create INFO data by population | 20190319 | 20230712 |
| vcfpeekvcf | Get the INFO from a VCF and use it for another VCF | 20150521 | 20240405 |
| vcfscanupstreamorf | Scan BAM for upstream-ORF. Inspired from https://github.com/ImperialCardioGenetics/uORFs | 20190218 | 20200804 |
| vcfserver | Web Server displaying VCF file. A web interface for vcf2table | 20171027 | 20220517 |
| vcfspliceai | Annotate VCF with spiceai web service | 20201107 | 20201107 |
| vcftbi2bed | extracts BED for each contig in a tabix-indexed VCF peeking first of last variant for each chromosome. | 20230214 | 20230214 |
| wib2bedgraph | Extract Wib files to bedgraph or wig | 20230819 | 20230819 |
VCF Manipulation
| Tool | Description | Creation | Update |
|---|---|---|---|
| bioalcidaejdk | java-based version of awk for bioinformatics | 20170712 | 20210412 |
| biostar130456 | Split individual VCF files from multisamples VCF file | 20150210 | 20200603 |
| builddbsnp | Build a DBSNP file from different sources for GATK | 20200904 | 2021070726 |
| findavariation | Finds a specific mutation in a list of VCF files | 20140623 | 20200217 |
| findgvcfsblocks | Find common blocks of calleable regions from a set of gvcfs | 20210806 | 20220401 |
| mantamerger | Merge Vcf from Manta VCF. | 20190916 | 20230320 |
| minicaller | Simple and Stupid Variant Caller designed for @AdrienLeger2 | 201500306 | 20220705 |
| swingvcfjexl | Filter VCF using Java Swing UI and JEXL/Javascript expression | 20220413 | 20220414 |
| swingvcfview | VCFviewer using Java Swing UI | 20210503 | 20210503 |
| vcf2intervals | split a vcf to interval or bed for parallelization | 20211112 | 20221128 |
| vcf2table | convert a vcf to a table, to ease display in the terminal | 20170511 | 20220507 |
| vcfallelebalance | Insert missing allele balance annotation using FORMAT:AD | 20180829 | 20200805 |
| vcfancestralalleles | Annotate 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.README | 20180418 | 20220126 |
| vcfbigbed | Annotate a VCF with values from a bigbed file | 20220107 | 20220107 |
| vcfbigwig | Annotate a VCF with values from a bigwig file | 20200506 | 20230819 |
| vcfburdenmaf | MAF for Cases / Controls | 20160418 | 202000713 |
| vcfcadd | Annotate 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. | 20140218 | 20220119 |
| vcfcombinetwosnvs | Detect 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 @AntoineRimbert | 20160215 | 20200425 |
| vcfcomposite | (in developpement) Finds Variants involved in a Het Compound Disease | 20170331 | 20200210 |
| vcfconcat | Concatenate VCFs with same sample. See also bcftools concat | 20131230 | 20240426 |
| vcfdistancevariants | Annotate variants with the distance between previous and next variant. | 20190410 | 20230510 |
| vcffiltergenes | Filter VEP/SnpEff Output from a list of genes. | 20160322 | 20230505 |
| vcffiltergtf | Filter VCF on GTF | 20230703 | 20230704 |
| vcffilterjdk | Filtering VCF with dynamically-compiled java expressions | 20170705 | 20220830 |
| vcffilterso | Filter a VCF file annotated with SNPEff or VEP with terms from Sequence-Ontology. Reasoning : Children of user's SO-terms will be also used. | 20170331 | 20200924 |
| vcfflatten | Flatten variants to one variant | 20230222 | 20230222 |
| vcfgenesplitter | Split VCF+VEP by gene/transcript. | 20160310 | 202220531 |
| vcfgnomad | Peek annotations from gnomad | 20170407 | 20231103 |
| vcfgnomadsv | Peek annotations from gnomad structural variants | 20190814 | 20211109 |
| vcfgrantham | add grantham score from annotated VCF variant | 20230503 | 20230503 |
| vcfhead | print the first variants of a vcf | 20131210 | 20200518 |
| vcfmulti2oneinfo | 'one variant with INFO with N values' to 'N variants with one INFO' | 20260106 | 20230524 |
| vcfpar | Flag human sexual regions excluding PAR. | 20200908 | 20200908 |
| vcfpeekaf | Peek the AF from another VCF | 20200624 | 20200904 |
| vcfphased01 | X10 Phased SVG to Scalar Vector Graphics (SVG) | 20190710 | 20230818 |
| vcfpolyx | Number of repeated REF bases around POS. | 20200930 | 20230526 |
| vcfrebase | Restriction sites overlaping variations in a vcf | 20131115 | 20200624 |
| vcfregulomedb | Annotate a VCF with the Regulome2 data (https://regulomedb.org/) | 20140709 | 20230512 |
| vcfsetdict | Set the ##contig lines in a VCF header on the fly |
20140105 | 20210201 |
| vcfshuffle | Shuffle a VCF | 20131210 | 20200818 |
| vcfsplitnvariants | Split VCF to 'N' VCF files | 202221122 | 202221201 |
| vcfspringfilter | Uses the java spring Framework to build complex vcf filters | 20230526 | 20230526 |
| vcfstats | Produce VCF statitics | 20131212 | 20230707 |
| vcfsvannotator | SV Variant Effect prediction using gtf, gnomad, etc | 20190815 | 20230509 |
| vcftail | print the last variants of a vcf | 20131210 | 20200518 |
| vcftrio | Find mendelian incompatibilitie / denovo variants in a VCF | 20130705 | 20200624 |
Retrocopy
| Tool | Description | Creation | Update |
|---|---|---|---|
| scanretrocopy | Scan BAM for retrocopies | 20190125 | 20230818 |
| starretrocopy | Scan retrocopies from the star-aligner/bwa output | 20190710 | 20191008 |
BAM Manipulation
| Tool | Description | Creation | Update |
|---|---|---|---|
| bam2haplotypes | Reconstruct SNP haplotypes from reads | 20211015 | 20211020 |
| bamphased01 | Extract Reads from a SAM/BAM file supporting at least two variants in a VCF file. | 20210218 | 20210218 |
| bamrenamechr | Convert the names of the chromosomes in a BAM file | 20131217 | 20191210 |
| bamstats04 | Coverage statistics for a BED file. | 20130513 | 20191003 |
| bamstats05 | Coverage statistics for a BED file, group by gene | 20151012 | 20210317 |
| bamwithoutbai | Query a Remote BAM without bai | 20191213 | 20191217 |
| basecoverage | 'Depth of Coverage' per base. | 20220420 | 20220420 |
| bioalcidaejdk | java-based version of awk for bioinformatics | 20170712 | 20210412 |
| biostar154220 | Cap BAM to a given coverage | 20150812 | 20210312 |
| biostar9566948 | Trim Reads So Only First Base Remains | 20230621 | 20230621 |
| findallcoverageatposition | Find 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 ? | 20141128 | 20210818 |
| sam2tsv | Prints the SAM alignments as a TAB delimited file. | 20170712 | 20210304 |
| samgrep | grep read-names in a bam file | 20130506 | 20210726 |
| samrmdupnames | remove duplicated names in sorted BAM | 20221207 | 20221207 |
| samviewwithmate | Extract reads within given region(s), and their mates | 20190207 | 20191004 |
| sortsamrefname | Sort a BAM on chromosome/contig and then on read/querty name | 20150812 | 20210312 |
| swingbamcov | Bam coverage viewer using Java Swing UI | 20210420 | 20220513 |
| swingbamview | Read viewer using Java Swing UI | 20220503 | 20230427 |
| texbam | Write text in a bam. Mostly for fun... | 20220708 | 20220708 |