This program parses a mpileup file to extract the coverage of each base at each position using specific phred and mapq cutoffs.
Beware that at the moment, the script only works with python 2.
python parseMPileup.py -i -p [-s] [-h]
- inputFile = Output from samtools pileup
- outputPrefix = Prefix used on output files
- -s = When True, the position file in created in a separated file
- -h = Help
Pascal Belleau and Astrid Deschênes