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.

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Install this software package

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Install vcfanno