JVARKIT

Java utilities for Bioinformatics

Warning

Since 2015-12-10, I'm slowly moving to a XML-based description of my tools and I'm now using java8 . I do my best to change all those tools. The documentation in the wiki migh be out of date. If you think you have found an error leave a message at https://github.com/lindenb/jvarkit/issues . Furthermore, I'm now using the "Apache Commons CLI library" for parsing the command line. For the arguments takings as input more than one parameter, you might have to add a double dash '--' to separate with the input files.

Author

Pierre Lindenbaum PhD

http://plindenbaum.blogspot.com

@yokofakun

Cite

see Cite

Download and install

See Download and Install

##Tools

Tool	Description
SplitBam	Split a BAM by chromosome group. Creates EMPTY bams if no reads was found for a given group.
SamJS	Filtering a SAM/BAM with javascript (rhino).
VCFFilterJS	Filtering a VCF with javascript (rhino)
SortVCFOnRef	Sort a VCF using the order of the chromosomes in a REFerence index.
Illuminadir	Create a structured (**JSON** or **XML**) representation of a directory containing some Illumina FASTQs.
BamStats04	Coverage statistics for a BED file. It uses the Cigar string instead of the start/end to compute the coverage
BamStats05	same as BamStats04 but group by gene
BamStats01	Statistics about the reads in a BAM.
VCFBed	Annotate a VCF with the content of a BED file indexed with tabix.
VCFPolyX	Number of repeated REF bases around POS.
VCFBigWig	Annotate a VCF with the data of a bigwig file.
VCFTabixml	Annotate a value from a vcf+xml file.4th column of the BED indexed with TABIX is a XML string.
GroupByGene	Group VCF data by gene/transcript.
VCFPredictions	Basic variant prediction using UCSC knownGenes.
FindCorruptedFiles	Reads filename from stdin and prints corrupted NGS files (VCF/BAM/FASTQ).
VCF2XML	Transforms a VCF to XML.
VCFAnnoBam	Annotate a VCF with the Coverage statistics of a BAM file + BED file of capture. It uses the Cigar string instead of the start/end to get the voverage
VCFTrio	Check for mendelian incompatibilities in a VCF.
SamGrep	Search reads in a BAM
VCFFixIndels	Fix samtools INDELS for @SolenaLS
NgsFilesSummary	Scan folders and generate a summary of the files (SAMPLE/BAM SAMPLE/VCF etc..).
NoZeroVariationVCF	creates a VCF containing one fake variation if the input is empty.
HowManyBamDict	for @abinouze : quickly find the number of distinct BAM Dictionaries from a set of BAM files.
ExtendBed	Extends a BED file by 'X' bases.
CmpBams	Compare two or more BAMs.
IlluminaFastqStats	Statistics on Illumina Fastqs
Bam2Raster	Save a BAM alignment as a PNG image.
VcfRebase	Finds restriction sites overlapping variants in a VCF file
FastqRevComp	Reverse complement a FASTQ file for mate-pair alignment
PicardMetricsToXML	Convert picards metrics file to XML.
Bam2Wig	Bam to Wiggle converter
TViewWeb	CGI/Web based version of samtools tview
VcfRegistryWeb	CGI/Web tool printing all variants at a given position for a collection VCF
BlastMapAnnots	Maps uniprot/genbank annotations on a blast result. See http://www.biostars.org/p/76056
VcfViewGui	Simple java-Swing-based VCF viewer.
BamViewGui	Simple java-Swing-based BAM viewer.
Biostar81455	Defining precisely the genomic context based on a position http://www.biostars.org/p/81455/
MapUniProtFeatures	map Uniprot features on reference genome.
Biostar86363	Set genotype of specific sample/genotype comb to unknown in multisample vcf file.
FixVCF	Fix a VCF HEADER when I forgot to declare a FILTER or an INFO field in the HEADER
Biostar78400	Add the read group info to the sam file on a per lane basis
Biostar78285	Extract regions of genome that have 0 coverage See http://www.biostars.org/p/78285/
Biostar77288	Low resolution sequence alignment visualization http://www.biostars.org/p/77288/
Biostar77828	Divide the human genome among X cores, taking into account gaps See http://www.biostars.org/p/77828/
Biostar76892	Fix strand of two paired reads close but on the same strand http://www.biostars.org/p/76892/
VCFCompareGT	VCF : compare genotypes of two or more callers for the same samples.
SAM4WebLogo	Creates an Input file for BAM + WebLogo.
SAM2Tsv	Tabular view of each base of the reads vs the reference.
Biostar84786	Table transposition
VCF2SQL	Generate the SQL code to insert a VCF into a database
VCFStripAnnotations	Removes one or more field from the INFO column from a VCF.
VCFGeneOntology	Finds and filters the GO terms for VCF annotated with SNPEFF or VEP
Biostar86480	Genomic restriction finder See http://www.biostars.org/p/86480/
BamToFastq	Shrink your FASTQ.bz2 files by 40+% using this one weird tip by ordering them by alignment to reference
PadEmptyFastq	Pad empty fastq sequence/qual with N/#
SamFixCigar	Replace 'M'(match) in SAM cigar by 'X' or '='
FixVcfFormat	Fix PL format in VCF. Problem is described in http://gatkforums.broadinstitute.org/discussion/3453
VcfToRdf	Convert a VCF to RDF.
VcfShuffle	Shuffle a VCF.
DownSampleVcf	Down sample a VCF.
VcfHead	Print the first variants of a VCF.
VcfTail	Print the last variants of a VCF
VcfCutSamples	Select/Exclude some samples from a VCF
VcfStats	Generate some statistics from a VCF
VcfSampleRename	Rename Samples in a VCF.
VcffilterSequenceOntology	Filter a VCF on Seqence Ontology (SO).
Biostar59647	position of mismatches per read from a sam/bam file (XML) See http://www.biostars.org/p/59647/
VcfRenameChromosomes	Rename chromosomes in a VCF (eg. convert hg19/ucsc to grch37/ensembl)
BamRenameChromosomes	Rename chromosomes in a BAM (eg. convert hg19/ucsc to grch37/ensembl)
BedRenameChromosomes	Rename chromosomes in a BED (eg. convert hg19/ucsc to grch37/ensembl)
BlastnToSnp	Map variations from a BLASTN-XML file.
Blast2Sam	Convert a BLASTN-XML input to SAM
VcfMapUniprot	Map uniprot features on VCF annotated with VEP or SNPEff.
VcfCompare	Compare two VCF files.
VcfBiomart	Annotate a VCF with the data from Biomart.
VcfLiftOver	LiftOver a VCF file.
BedLiftOver	LiftOver a BED file.
VcfConcat	Concatenate VCF files.
MergeSplittedBlast	Merge Blast hit from a splitted database
FindMyVirus	Virus+host cell : split BAM into categories.
Biostar90204	linux split equivalent for BAM file .
VcfJaspar	Finds JASPAR profiles in VCF
GenomicJaspar	Finds JASPAR profiles in Fasta
VcfTreePack	Create a TreeMap from one or more VCF
BamTreePack	Create a TreeMap from one or more Bam.
FastqRecordTreePack	Create a TreeMap from one or more Fastq files.
WorldMapGenome	Map bed file to Genome + geographic data.
AddLinearIndexToBed	Use a Sequence dictionary to create a linear index for a BED file. Can be used as a X-Axis for a chart.
VCFComm	Compare mulitple VCF files, ouput a new VCF file.
VcfIn	Prints variants that are contained/not contained into another VCF
Biostar92368	Binary interactions depth See also http://www.biostars.org/p/92368
VCFCombineTwoSnvs	TODO
FastqGrep	Finds reads in fastq files
VcfCadd	Annotate a VCF with Combined Annotation Dependent Depletion (CADD) data.
SortVCFOnInfo	sort a VCF using a field in the INFO column
SamChangeReference	TODO
SamExtractClip	TODO
GCAndDepth	Extracts GC% and depth for multiple bam using a sliding window.
MsaToVcf	Getting a VCF file from a CLUSTAW or FASTA alignment
CompareBamAndBuild	Compare two BAM files mapped on two different builds. Requires a liftover chain file.
KnownGenesToBed	Convert UCSC KnownGene to BED.
Biostar95652	Drawing a schematic genomic context tree. See also http://www.biostars.org/p/95652/
SamToPsl	Convert SAM/BAM to PSL or BED12 .
BWAMemNOp	merge the SA:Z:* attributes of a read mapped with bwa-mem and prints a read containing a cigar string with 'N' (Skipped region from the REF).
FastqEntropy	Compute the Entropy of a Fastq file (distribution of the length(gzipped(sequence)))
NgsFilesScanner	Build a persistent database of NGS file. Dump as XML.
SigFrame	GUI displaying CGH data
Biostar103303	Calculate Percent Spliced In (PSI)
VCFComparePredictions	Compare the variant predictions of VCFs
BackLocate	Map a position in a protein back to the genomic coordinates.
FindAVariation	Search for variations in a set of VCF files.
AlleleFrequencyCalculator	VCF: Alelle Frequency Calculator
BuildWikipediaOntology	Build a simple RDFS/XML ontology from Wikipedia Categories.
AlmostSortedVcf	Sort an 'almost' sorted VCF using an in-memory buffer.
Biostar105754	bigwig: peak distance from specific genomic BED region
VcfRegulomeDB	Annotate a VCF with the RegulomeDB data (http://regulome.stanford.edu/)
Biostar106668	unmark duplicates (deprecated)
BatchIGVPictures	GUI: Batch pictures with IGV
PubmedDump	Dump pubmed data as XML.
BamIndexReadNames	Build a dictionary of read names to be searched with BamQueryReadNames.
BamQueryReadNames	Query a Bam file indexed with BamIndexReadNames.
FastqShuffle	Shuffle Fastq files.
FastqSplitInterleaved	Split interleaved Fastq files
PubmedFilterJS	Filters pubmed XML using javascript.
ReferenceToVCF	Creates a VCF containing all possible substitutions in a Reference Genome..
VcfEnsemblReg	Annotate a VCF with the UCSC genome hub tracks for Ensembl Regulation.
FastqJS	Filters a FASTQ file using javascript.
Bam2SVG	Convert a BAM to SVG
LiftOverToSVG	Convert UCSC LiftOver chain files to animated SVG
VCFMerge	Combines VCF files.
FixVcfMissingGenotypes	Use BAM to fill missing genotypes in merged VCFs
NcbiTaxonomyToXml	Dump NCBI taxonomy tree as a hierarchical XML document
BamCmpCoverage	Creates the figure of a comparative view of the depths sample vs sample
FindAllCoveragesAtPosition	Find depth at specific position in a list of BAM files
VcfMultiToOne	Convert VCF with multiple samples to a VCF with one SAMPLE
Evs2Xml	Download data from Exome Variant Server as XML.
VcfRemoveGenotypeIfInVcf	Reset Genotypes in VCF if they've been found in another VCF indexed with tabix
Biostar130456	Generate one VCF file for each sample from a multi-samples VCF
UniprotFilterJS	Filter Uniprot XML with a javascript expression.
SkipXmlElements	Filter XML elements with a javascript expression.
MiniCaller	Simple and Stupid Variant Caller designed for @AdrienLeger2
VcfCompareCallersOneSample	For my colleague Julien. Compare VCF allers with VCF with one sample.
SamRetrieveSeqAndQual	Is there a tool to add seq and qual to BAM? for @sjackman
VcfEnsemblVepRest	Annotate a VCF with Ensembl REST API.
VcfCompareCallers	Compare two VCFs and print common/exclusive information for each sample/genotype
BamStats02	Generate and explore statistics about the reads in a BAM (Sample/File/Flags/chroms/MAPQ)
BamTile	Bam tiling Path.
XContaminations	for @AdrienLeger2 : test for cross contamination between samples in same flowcell/runlane.
VCFJoinVcfJS	Join two VCF files using javascript.
Biostar139647	Convert Clustal/Fasta alignment to SAM/BAM
BioAlcidae	Reformat bioinformatics files using javascript/rhino (~ awk)
VCFBedSetFilter	Set FILTER for VCF having intersection with BED
VCFReplaceTag	Replace the key in INFO/FORMAT/FILTER
VcfIndexTabix	sort, Compress (bgz) a VCF and create tabix index on the fly.
VcfPeekVcf	Peek INFO Tag and ID from another VCF
VcfGetVariantByIndex	Access a (plain or tabix-indexed) VCF file by the i-th index.
VcfMultiToOneAllele	VCF: "one variant with N ALT alleles" to "N variants with one ALT"
VcfMultiToOneInfo	VCF: "one variant having INFO with N values" to "N variants having INFO with one value"
BedIndexTabix	Index and sort a BED on the fly with Tabix
VcfToHilbert	Plot a Hilbert Curve from a VCF file.
Biostar145820	Shuffl Bam/Subsample BAM to fixed number of alignments
PcrClipReads	Soft clip BAM files based on PCR target regions https://www.biostars.org/p/147136/
ExtendReferenceWithReads	Extending ends of REF sequence with the help of reads in BAM https://www.biostars.org/p/148089/
PcrSliceReads	Mark PCR reads to their PCR amplicon https://www.biostars.org/p/149687/"
SamJmx	Monitor/interrupt/break a BAM/SAM stream with java JMX
VcfJmx	Monitor/interrupt/break a VcfJmx stream with java JMX
Gtf2Xml	convert gff to XML in order to be processed with XSLT
SortSamRefName	Sort a SAM/BAM on REF/contig and then on read/query name
Biostar154220	Cap BAM to a given coverage. see https://www.biostars.org/p/154220
VcfToBam	create a BAM from a VCF.
Biostar165777	Split a XML file (e.g: blast)
BlastFilterJS	Filters a XML Blast Output with a javascript expression
Biostar170742	SAM to AXT converter
Biostar172515	Convert Bam Index to XML
Biostar173114	make a bam file smaller by removing unwanted information see also https://www.biostars.org/p/173114
SamSlop	extends the SAM record in 5' and 3'
Biostar175929	Construct a combination set of fasta sequences from a vcf
VcfCalledWithAnotherMethod	Add flags in VCF to tell whether Genotype/variant was called in another VCF
Biostar178713	split bed file into several bed files where each region is separated of any other by N bases
VcfRemoveGenotypeJs	Reset Genotypes in VCF using a javascript expression