WGAbed - a package for handling whole genome alignments
About
This packages handles the conversion of a whole genome alignment file in MAF format to a reference ordered BED format containing all the information in the MAF file but in a more accessible format. This repository contains scripts for creating a 'whole genome alignment BED' or 'WGAbed' file as well as scripts for downstream manipulation of the file.
The package was conceived and implemented by Pádraic Corcoran (https://github.com/padraicc), with additions and later implemented scripts by Henry Barton (https://github.com/henryjuho).
Documentation
Documentation for the package can be found at: https://henryjuho.github.io/WGAbed.
Running
The package requires the pysam module: http://pysam.readthedocs.io/en/latest/index.html.
To obtain the package code issue:
git clone https://github.com/henryjuho/WGAbed.git