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.\" Automatically generated by Pandoc 2.7.3
.\"
.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
.B \f[B]0\f[R]
Success
.TP
.B \f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2020 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.
|
