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

# vcfprimers(1)

## NAME

**vcfprimers**

## SYNOPSIS

**vcfprimers** options

## DESCRIPTION

For each VCF record, extract the flanking sequences, and write them to stdout as FASTA records suitable for alignment.

## OPTIONS

-

  ```
  options:
      -f, --fasta-reference  FASTA reference file to use to obtain primer sequences
      -l, --primer-length    The length of the primer sequences on each side of the variant
  This tool is intended for use in designing validation
  experiments.  Primers extracted which would flank all of the alleles at multi-allelic
  sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
  The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
  for example:
  >20_233255_LEFT
  CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
  >20_233255_RIGHT
  ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
  Type: transformation
  ```

## 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.