Pipeline Options

MTOOLBOX PROGRAMS OPTIONS

Besides the mandatory -i option, the execution of MToolBox can be fine-tuned by tweaking parameters of the mapExome.py and assembleMTgenome.py scripts by running MToolBox as follows:

MToolBox.sh -i <config.sh> -m "<mapExome_options>" -a "<assembleMTgenome_options>"

Most relevant options:

-t (mapExome.py) to set the number of threads used by gsnap. Default is 8.

-t (assembleMTgenome.py) to set the minimum distance from the read end required to retain an indel for variant calling. Default is 5. Please note that only values >= 5 are allowed.

-z (assembleMTgenome.py) to set the minimum heteroplasmy threshold for variants to be reported in the FASTA consensus sequence. Default is 0.80.

For the full list of MToolBox options, please run as follows:

MToolBox.sh -h

For the full list of mapExome and assembleMTgenome options, please run as follows:

mapExome.py -h
assembleMTgenome.py -h

Usage examples:

MToolBox.sh -i test_config.sh -m "-t 20" -a "-t 10 -z 0.6"

This command will run MToolBox on the set of samples specified within the test_config.sh file, setting the number of GSNAP threads 20 (-m "-t 20.."), the minimum nucleotide distance allowed from read end to retain indels to 10 (-a "-t 10") and the heteroplasmy threshold to retain nucleotide variants in the FASTA consensus sequence of 0.6 (-a "-z 0.6").