---
name: "vcfremap"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/vcfremap"
---

# 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)](/vcflib/1.md)

## 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.