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[ Source: vcfanno  ]

Package: vcfanno (0.3.2+ds-2 and others)

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annotate a VCF with other VCFs/BEDs/tabixed files

Vcfanno allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.

  * For VCF, values are pulled by name from the INFO field with special
    cases of ID and FILTER to pull from those VCF columns.
  * For BED, values are pulled from (1-based) column number.
  * For BAM, depth (count), "mapq" and "seq" are currently supported.

Vcfanno is written in go and it supports custom user-scripts written in Lua. It can annotate more than 8000 variants per second with 34 annotations from 9 files on a modest laptop and over 30K variants per second using 12 processes on a server.

Other Packages Related to vcfanno

  • depends
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Download vcfanno

Download for all available architectures
Architecture Version Package Size Installed Size Files
amd64 0.3.2+ds-2+b6 2,103.4 kB6,786.0 kB [list of files]
arm64 0.3.2+ds-2+b6 1,785.3 kB6,321.0 kB [list of files]
armel 0.3.2+ds-2+b6 1,821.7 kB5,766.0 kB [list of files]
armhf 0.3.2+ds-2+b6 1,814.7 kB5,766.0 kB [list of files]
i386 0.3.2+ds-2+b6 1,980.7 kB5,764.0 kB [list of files]
mips64el 0.3.2+ds-2+b6 1,671.5 kB6,915.0 kB [list of files]
mipsel 0.3.2+ds-2+b6 1,695.4 kB6,442.0 kB [list of files]
ppc64el 0.3.2+ds-2+b6 1,746.0 kB6,321.0 kB [list of files]
s390x 0.3.2+ds-2+b6 1,922.7 kB6,708.0 kB [list of files]