Tool:Vcflib Documentation
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11.2 years ago
Erik Garrison ★ 2.4k

I've been working on vcflib for some time, but never drafted a single piece of documentation to cover its implemented functions.

vcflib documentation/manual: https://github.com/ekg/vcflib#vcflib

I hope this begins to clarify some of the possible ways to use the features in the library, which include:

  • filtering (vcffilter, vcfsom)
  • validation (vcfcheck)
  • intersection, union, comparison (vcfintersect)
  • cross-file annotation (vcfannotate, vcfintersect)
  • sample manipulation (vcfkeepsamples, vcffixup, vcfglxgt, vcfcommonsamples)
  • sequence manipulation (vcfcleancomplex, vcfbreakmulti, vcfprimers)
  • extracting statistics (vcfstats)
  • haplotype visualization and remapping (vcfremap)
  • haplotype composition (vcfgeno2haplo) and decomposition (vcfallelicprimitives)
  • unsupervised classification of variants (vcfsom)
  • random sampling (vcfrandomsample)
  • somatic vs. germline tagging (vcfsamplediff)
  • sorting (vcfstreamsort)

These tools have been designed to work on VCF streams, and both uncompressed or BGZIP-compressed (+tabixed) VCF files. Many complex queries can be executed simply by combining component tools in serial.

vcf • 11k views
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Hi Erik, I am trying to use vcfbreakmulti. I would like to know the options which I can use in the command mentioned below. The readme file which is part of vcflib directory while I cloned using git also has limited info about it. "vcfbreakmulti [options] [file]"

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Please let me know if you find an answer because I am facing the same problem.

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I need to filter my vcf file to include only variants that have at least 30 individuals in each of the possible genotypes is it possible to do this with Vcflib. Thanks!

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