fix.lofreq.af {varitas}

fix.lofreq.af

Description

LoFreq also does not output allele frequencies, so this script calculates them from the DP (depth) and AD (variant allele depth) values–which are also not output nicely– and adds them to the annotated vcf.

Usage

fix.lofreq.af(variant.specification)

Arguments

variant.specification

Data frame of variant file information