#mutools
##Description A suite of tools for working with MuTect.
##Dependencies
- pysam
- argparse *if your python version is < 2.7
- futures
- multimutect requires that python 2 be used, as pysam is written in it.
##Required Files
##Typical Workflow You'd most likely make use of the tools in premutect to prepare BAM files first. First you'd use addgroups.py to add (or replace) read groups within the BAM files of the directory you specified. Then you would sort them using reorder_all.py. You must have a FASTA file sorted in coordinate order for this to work, however.
Next, you would build bam indices using reindex.py. And finally, if MuTect complains about unmapped reads (or if you are simply unsure about them) you can use mapqto0.py to set MAPQ to 0 for all unmapped reads.
This should be sufficient to prepare your BAM files for processing by MuTect.
The postprocessing steps are different depending on how you go about running multimutect. If you didn't use the --process_whole_bam option, you will need to run catenate.py on your directory before combine.py, otherwise combine.py is enough. If you've just processed a directory filled with chromosomal regions (i.e., chromosome1.bam, chromosome2.bam...) with the --process_whole_bam option, however, you will only need to run catenate.py with the --listfile option. Either way, appropriate processing will produce a single VCF file with columns corresponding to each sample used in MuTect's analysis.
Unless you use an option provided by combine.py, you will also have a leftover directory of VCF files. I leave this choice up to the user, as multiple VCF files may be desired and the combine phase may be omitted entirely.
Further documentation for each tool is contained within README files inside their respective directories.
##Installation
Simply execute ./install.sh after making it executable with
chmod 755 install.sh (if it isn't already). This will make an alias
for each utility within your bashrc. Then, execute source ~/.bashrc to
"activate" these changes in your current shell. This will let you
use the suite of tools without having to specify absolute paths to the
files in the installation directory. For instance, this command line
would be possible anywhere:
multimutect -f hg19.fa -b bamfiles.txt -i mysamples -o outputvcfs