SplitByChromosome

Python wrapper for samtools which will split a BAM file into standard chromosomes (1-22, X, Y) in parallel

This python script spawns multiple processes of samtools to split a bam file by chromosome in parallel. Because this is executing 24 jobs simultaneously it is best to execute this as a batch script on the bynode queue as it should use all of the available cores.

Usage: python3 split_by_chromosome.py [-h] [--chr] input.bam Input bam must be coordinate sorted and have a .bai index file.

Requirements

• Samtools must be installed and present on the PATH
• Python3.5 (I have not tested it with python 2.7)

Options

-h Display help

--chr Set this flag if your bam file is aligned to a genome where chromosomes start with 'chr'

Created by Anthony Scott Sep 9, 2017