SYNOPSIS

reapr pipeline [options] <assembly.fa> <in.bam> <outdirectory> [perfectmapprefix]

DESCRIPTION

[perfectmapprefix] is optional and should be the prefix used when task perfectmap was run.

It is assumed that reads in <in.bam> are 'innies', i.e. the correct orientation is reads in a pair pointing towards each other (--→ ←--).

OPTIONS

-stats|fcdrate|score|break option=value

You can pass options to stats, fcdrate, score or break if you want to change the default settings. These can be used multiple times to use more than one option. e.g.:
  -stats i=100 -stats j=1000 If an option has no value, use 1. e.g.
  -break b=1

-fcdcut <float>

Set the fcdcutoff used when running score. Default is to run fcdrate to determine the cutoff. Using this option will skip fcdrate and use the given value.

-x

By default, a bash script is written to run all the pipeline stages. Using this option stops the script from being run.