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% VCFREMAP(1) vcfremap (vcflib) | vcfremap (VCF transformation)
% Erik Garrison and vcflib contributors
# NAME
**vcfremap**
# SYNOPSIS
**vcfremap** [options] [<vcf file>]
# 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](./vcflib.md)(1)
# OTHER
## Source code
[vcfremap.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcfremap.cpp)
# LICENSE
Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.
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