NAME

SYNOPSIS

DESCRIPTION

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

OTHER

LICENSE

AUTHORS