flankextractor

Extracts and processes sequence flanking alleles of interest.

Overview

Flankextractor is a simple command-line tool that takes a list of variants in VCF/BCF format and uses their coordinates to extract flanking sequences from a reference FASTA file. This reference FASTA file must be the same reference used to align and call the variants. By default, flankextractor will output sequences for both the reference and alternate alleles. This behaviour can be changed using the ‘--alleles ref|alts’ option.

Flankextractor uses pysam under the hood to parse the VCF and FASTA files and biopython to create, process and output the flanking sequences.

Installation

Flankextractor is available through pypi. To install, type:

pip install flankextractor