% VCFPRIMERS(1) vcfprimers (vcflib) | vcfprimers (VCF transformation)
% Erik Garrison and vcflib contributors

# NAME

**vcfprimers**

# SYNOPSIS

**vcfprimers** [options] <vcf file>

# 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](./vcflib.md)(1)



# OTHER

## Source code

[vcfprimers.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcfprimers.cpp)

# LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

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