NAME

       vcfremap

SYNOPSIS

       vcfremap options []

DESCRIPTION

       For  each alternate allele, attempt to realign against the reference with lowered gap open
       penalty.  If realignment is possible, adjust the cigar  and  reference/alternate  alleles.
       Observe  how different alignment parameters, including context and entropy-dependent ones,
       influence variant classification and interpretation.

OPTIONS

              options:
                  -w, --ref-window-size N      align using this many bases flanking each side of the reference allele
                  -s, --alt-window-size N      align using this many flanking bases from the reference around each alternate allele
                  -r, --reference FILE         FASTA reference file, required with -i and -u
                  -m, --match-score N          match score for SW algorithm
                  -x, --mismatch-score N       mismatch score for SW algorithm
                  -o, --gap-open-penalty N     gap open penalty for SW algorithm
                  -e, --gap-extend-penalty N   gap extension penalty for SW algorithm
                  -z, --entropy-gap-open       use entropy scaling for the gap open penalty
                  -R, --repeat-gap-extend N    penalize non-repeat-unit gaps in repeat sequence
                  -a, --adjust-vcf TAG         supply a new cigar as TAG in the output VCF

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.