VCFREMAP(1)

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

AUTHORS
Erik Garrison and vcflib contributors.