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)