RJE SAMtools parser and processor
Copyright © 2013 Richard J. Edwards - See source code for GNU License Notice
See SLiMSuite Blog for further documentation. See
The initial function of this program is for calling/assessing genetic changes following MPileup mapping of a wildtype (e.g. ancestor) and mutant (BAM file) against the same reference genome. The MPileup files should be generated by piping the output of the following into a file:
samtools mpileup -BQ0 -d10000000 -f <Ref Genome Fasta> <BAM file>
NOTE: This version has been "frozen" as V0. Development continuing with V1.0.0.
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation. # 0.1.0 - Modified version to handle multiple loci per file. (Original was for single bacterial chromosomes.) # 0.2.0 - Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.