NAME

       quality_check - perform a sanity check on the mapping results (SAM file)

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: ./]

quality_check SVNr18                              February 2014                                 QUALITY_CHECK(1)