SYNOPSIS

quality_check [Options] SAMFILE

DESCRIPTION

Perform a sanity check on the mapping results (SAM file).

This tool analyzes the output of the read mapper and provides useful information to the user to decide whether the set of reference sequences and the mapper settings are feasible for the given dataset.

OPTIONS

SAMFILE

Name of the SAM file to analyze

-h, --help

show this help message and exit

-o OUT, --outpath=OUT

Path to the directory for the analysis output. [default: ./]