Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs...

Here are a few tools I recently wrote (and reinvented) for Jvarkit.

BamViewGui

a simple java-Swing-based BAM viewer.

VcfShuffle

Shuffle a VCF.

GroupByGene

Group VCF data by Gene

$ curl -s -k "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\
java -jar dist/groupbygene.jar |\
head | column  -t

#chrom  min.POS    max.POS    gene.name  gene.type         samples.affected  count.variations  M10475  M10478  M10500  M128215
chr10   52004315   52004315   ASAH2      snpeff-gene-name  2                 1                 0       0       1       1
chr10   52004315   52004315   ASAH2      vep-gene-name     2                 1                 0       0       1       1
chr10   52497529   52497529   ASAH2B     snpeff-gene-name  2                 1                 0       1       1       0
chr10   52497529   52497529   ASAH2B     vep-gene-name     2                 1                 0       1       1       0
chr10   48003992   48003992   ASAH2C     snpeff-gene-name  3                 1                 1       1       1       0
chr10   48003992   48003992   ASAH2C     vep-gene-name     3                 1                 1       1       1       0
chr10   126678092  126678092  CTBP2      snpeff-gene-name  1                 1                 0       0       0       1
chr10   126678092  126678092  CTBP2      vep-gene-name     1                 1                 0       0       0       1
chr10   135336656  135369532  CYP2E1     snpeff-gene-name  3                 2                 0       2       1       1

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. The ouput is a XML file that can be processed with xslt.

$ curl  "https://raw.github.com/arq5x/gemini/master/test/test4.vep.snpeff.vcf" |\
  java -jar dist/vcfstats.jar |\
  xmllint --format -

<?xml version="1.0" encoding="UTF-8"?>
<vcf-statistics version="314bf88924a4003e6d6189ad3280d8b4df485aa1" input="stdin" date="Thu Dec 12 16:20:14 CET 2013">
  <section name="General">
    <statistics name="general" description="general">
      <counts name="general" description="General" keytype="string">
        <property key="num.dictionary.chromosomes">93<
         (...)

That's it,

Pierre