NAME

       propmapped - calculate the proportion of mapped reads/fragments

USAGE

       prommapped [options] -i <file>

       Required arguments:

       -i <string>
              An input file containing read mapping results. Both SAM or BAM formats are supported.

       Optional arguments:

       -o <string>
              Name of output file including mapping statistics.

       -f     If  specified,  fragments (read pairs) will be counted instead of individual reads. This option is
              only applicable for paired-end reads.

       -p     If specified, only properly paired reads will be counted.  This  option  is  only  applicable  for
              paired-end reads.

propmapped 1.5.0-p1+dfsg-2                        January 2016                                     PROPMAPPED(1)