Module: rje_samtools_V0 Description: RJE SAMtools parser and processor Version: 0.2.0 Last Edit: 21/12/15

Copyright © 2013 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_obj rje_zen

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

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.

Commandline

wtpileup=FILE : MPileup results for wildtype genome resequencing [None]
mutpileup=FILE : MPileup results for mutant genome resequencing [None]
qcut=X : Min. quality score for a call to include [40]
ignoren=T/F : Whether to exclude "N" calls for major/minor alleles [True]
minfreq=X : Minor allele(s) frequency correction for zero counts (e.g. Sequencing error) [0.001]
majdif=T/F : Whether to restrict output and stats to positions with Major Allele differences [True]
majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]
snptables=LIST : Existing SNPs of interest to be cross-referenced with the WT and Mutant SNPs []

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]