VCFFIXUP(1)

NAME

vcffixup

SYNOPSIS

vcffixup

DESCRIPTION

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 VALUES

0   Success

not 0
    Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.