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]