reapr-stats1
Generate reapr stats from a bam file
Usage
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)
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.