vcfcheck.md

% VCFCHECK(1) vcfcheck (vcflib) | vcfcheck (VCF metrics) % Erik Garrison and vcflib contributors

NAME

vcfcheck

SYNOPSIS

vcfcheck [options]

DESCRIPTION

Validate integrity and identity of the VCF by verifying that the VCF record's REF matches a given reference file.

OPTIONS

options:

    -f, --fasta-reference  FASTA reference file to use to obtain primer sequences.
    -x, --exclude-failures If a record fails, don't print it.  Otherwise do.
    -k, --keep-failures    Print if the record fails, otherwise not.
    -i, --ignore-case      Ignore case differences between FASTA reference and vcf.
    -h, --help             Print this message.
    -v, --version          Print version.

Type: metrics

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

vcfcheck.cpp

LICENSE

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