NAME

       reapr-stats - generate REAPR stats from a BAM file

SYNOPSIS

       reapr stats [options] <preprocess-output-directory> <outprefix>

OPTIONS

       -f <int>
           Insert size [ave from stats.txt]

       -i <int>
           Minimum insert size [pc1 from stats.txt]

       -j <int>
           Maximum insert size [pc99 from stats.txt]

       -m <int>
           Maximum read length (this doesn’t need to be exact, it just determines memory allocation, so must be
           >= max read length) [2000]

       -p <string>
           Name of .gz perfect mapping file made by perfectmap

       -q <int>
           Ignore reads with mapping quality less than this [0]

       -s <int>
           Calculate FCD error every n-th base [ceil((fragment size) / 1000)]

       -u <string>
           File containing list of chromosomes to look at (one per line)

SEE ALSO

       reapr(1)

                                                                                                  REAPR-STATS(1)