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JVARKIT specifications

Information


Unique identifier OMICS_24364
Name JVARKIT
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format VCF, BED, SAM, BAM, CLUSTAW, FASTA, FASTQ, TBI, BAI
Output format VCF, FASTQ, XML, SAM, BAM, BED, FASTA, PSL, JSON, RDF, GFF
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Advanced
Version KnimeHelper-2017-11-20
Stability Stable
Maintained Yes

Subtools


  • bam2svg
  • bioalcidae
  • bioalcidaejdk
  • biostar77288
  • PcrClipReads
  • sam2tsv
  • sam4weblogo
  • samjdk
  • samjs
  • sigframe
  • vcffilterjdk
  • vcffilterjs

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Versioning


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Documentation


Maintainer


  • person_outline Pierre Lindenbaum <>

Additional information


http://lindenb.github.io/jvarkit/

Publication for JVARKIT

JVARKIT in pipelines

 (2)
2015
PMCID: 4606740
PMID: 26469882
DOI: 10.1038/srep15223

[…] step, were removed. the resulting genome sequences, along with those ev-d68 genomes publicly available in genbank, were compared using the clustal x (version 2.1). the biostar94573 algorithm of jvarkit (https://github.com/linden/jvarkit/wiki/biostar94573) was used to generate a variant call format file (.vcf) from the clustal multi-sequence alignment file (.aln). the vcftools suite was used […]

2014
PMCID: 4154752
PMID: 25188499
DOI: 10.1371/journal.pone.0106689

[…] data from the drosophila genetic reference panel (dgrp) to estimate both the rate of residual heterozygosity as well as a corrected error rate of the truseq synthetic long-reads. we applied the jvarkit utility to identify positions in the reference genome where mismatches occurred. we then used the relationship that the total number of sites with mismatches to the euchromatic reference […]


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JVARKIT in publications

 (8)
PMCID: 5898910
PMID: 29578408
DOI: 10.7554/eLife.34042.036

[…] from protein domain databases (superfamily, smart, pfam and prosite). protein modifications were downloaded from uniprot () and mapped to mm10 using backlocate software (http://lindenb.github.io/jvarkit/). genomic coordinates of protein modifications were then overlapped with alternative 3’utr isoforms to find those that are unique to the long isoform., to analyze the relationship […]

PMCID: 5850729
PMID: 29048557
DOI: 10.1093/molbev/msx274

[…] power in detecting linkage of the editing events., for each bam sequence alignment file, we extracted all the uniquely mapped reads spanning at least two editing sites with samtools 1.3.1 () and sam2tsv (). soft clipping bases in the alignments were not considered, and reads spanning only one editing sites were discarded. in each sample, we required the editing sites to have sequencing […]

PMCID: 5147911
PMID: 27936026
DOI: 10.1371/journal.pone.0167600

[…] was performed with samtools [] phase version 0.1.19 on the two sets of extracted records., miseq read pairs were extracted and assigned from the miseq bam file using a combination of bedtools and jvarkit git commit 865252a [, ] at the private variants (12 snps and 2 indels) in the single contributor datasets (). the read pairs were sorted into three pools of extracted reads, being shared, […]

PMCID: 5137419
PMID: 27431325
DOI: 10.1093/nar/gkw649

[…] the shortrna library preparation aligning to the flt 3′ end were stripped of adapter sequences using cutadapt, examined for the presence of untemplated sequences using the samextractclip tool of the jvarkit package, and the nucleotide composition was assessed with a custom script., to achieve efficient knockdown of tut4 and tut7 expression in hek293 cell lines producing different dis3l2 […]

PMCID: 4896128
PMID: 27271295
DOI: 10.1038/sdata.2016.25

[…] and graphmap (version 0.22, parameters: default/semiglobal bit-vector alignment mode). cigar strings in the generated bam files were updated to the x/= format using the samfixcigar module of the jvarkit package (https://github.com/lindenb/jvarkit/wiki/samfixcigar). error rates were calculated according to the gigar strings using a modified version of count-errors.py […]


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JVARKIT institution(s)
Institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France

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