Provided by: libvcflib-tools_1.0.3+dfsg-1_amd64 bug

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 2011-2022 (C) Erik Garrison and vcflib contributors.  MIT licensed.


AUTHORS
       Erik Garrison and vcflib contributors.