| REAPR-STATS(1) | REAPR-STATS(1) |
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)