vcffixup1

Usage

Overview

Generates a VCF stream where AC and NS have been generated for each record using sample genotypes

Options

Count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.)
Uses genotypes from the VCF file to correct AC (alternate allele count), AF
(alternate allele frequency), NS (number of called), in the VCF records.  For
example:
    % vcfkeepsamples file.vcf NA12878 | **vcffixup** - | vcffilter -f "AC > 0"
Would downsample file.vcf to only NA12878, removing sites for which the sample
was not called as polymorphic.
Type: transformation

Exit status

0

Success

not 0

Failure

Other