Provided by: libvcflib-tools_1.0.9+dfsg1-3build1_amd64 bug

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.