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.TH "VCFREMAP" "1" "" "vcfremap (vcflib)" "vcfremap (VCF transformation)"
.hy
.SH NAME
.PP
\f[B]vcfremap\f[R]
.SH SYNOPSIS
.PP
\f[B]vcfremap\f[R] options []
.SH DESCRIPTION
.PP
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.
.SH OPTIONS
.IP
.nf
\f[C]
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

\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.