VCFPRIMERS(1)

NAME

vcfprimers

SYNOPSIS

vcfprimers options

DESCRIPTION

For each VCF record, extract the flanking sequences, and write them to stdout as FASTA records suitable for alignment.

OPTIONS

    options:
        -f, --fasta-reference  FASTA reference file to use to obtain primer sequences
        -l, --primer-length    The length of the primer sequences on each side of the variant
    This tool is intended for use in designing validation
    experiments.  Primers extracted which would flank all of the alleles at multi-allelic
    sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
    The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
    for example:
    >20_233255_LEFT
    CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
    >20_233255_RIGHT
    ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
    Type: transformation

EXIT VALUES

0   Success

not 0
    Failure

SEE ALSO

vcflib(1)

OTHER

LICENSE

Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS
Erik Garrison and vcflib contributors.