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PROPMAPPED(1) User Commands PROPMAPPED(1)

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 v1.6.3

Calculate the proportion of mapped reads/fragments.
January 2019 propmapped 1.6.3+dfsg