Man page - vcfremap(1)
Packages contas this manual
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Package: libvcflib-tools
apt-get install libvcflib-tools
apt-get install libvcflib-tools
Manuals in package:
Documentations in package:
Manual
| VCFREMAP(1) | vcfremap (VCF transformation) | 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 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.
AUTHORS
Erik Garrison and vcflib contributors.
| vcfremap (vcflib) |