| REAPR-SCORE(1) | REAPR-SCORE(1) |
NAME¶
reapr-score - calculate scores and assembly errors
SYNOPSIS¶
reapr score [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>
OPTIONS¶
-f <int>
Minimum inner fragment coverage [1]
-g <int>
Max gap length to call over [0.5 *
outer_mean_insert_size]
-l <int>
Length of window [100]
-p <int>
Use perfect mapping reads score with given min coverage.
Incompatible with -P.
-P <int>
Same as -p, but force the score to be zero at any
position with at least the given coverage of perfect mapping reads and which
has an OK insert plot, , i.e. perfect mapping reads + insert distribution
override all other tests when calculating the score. Incompatible with
-p.
-q <float>
Max bad read ratio [0.33]
-r <int>
Min read coverage [max(1, mean_read_cov - 4 *
read_cov_stddev)]
-R <int>
Repeat calling cutoff. -R N means call a repeat if
fragment coverage is >= N times (expected coverage). Use -R 0 to not call
repeats [2]
-s <int>
Min score to report in errors file [0.4]
-u <int>
FCD error window length for error calling [insert_size /
2]
-w <float>
Min percentage of bases in window needed to call as bad
[0.8]