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.TH "VCFFIXUP" "1" "" "vcffixup (vcflib)" "vcffixup (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]vcffixup\f[R]
.SH SYNOPSIS
.PP
\f[B]vcffixup\f[R]
.SH DESCRIPTION
.PP
Generates a VCF stream where AC and NS have been generated for each
record using sample genotypes
.SH OPTIONS
.IP
.nf
\f[C]



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 \[dq]AC > 0\[dq]

Would downsample file.vcf to only NA12878, removing sites for which the sample
was not called as polymorphic.

Type: transformation
\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.