NAME

       reapr-perfectfrombam - generate perfect mapping plots from a bam file

SYNOPSIS

       reapr perfectfrombam [options] <in.bam> <outfileprefix> <mininsert> <maxinsert>
       <repetitive-max-qual> <perfect-min-qual> <perfect-min-alignment-score>

DESCRIPTION

       Alternative to using perfectmap, for large genomes.

       Takes a BAM, which must have AS:... tags in each line. Makes file of perfect mapping
       depth, for use with the REAPR pipeline. Recommended to use perfectmap instead, unless your
       genome is large (more than ~300MB), since although very fast to run, 'reapr perfectmap'
       uses a lot of memory.

       A BAM file made by smaltmap is suitable input.

       Reads in pair pointing towards each other, with the given minimum alignment score and
       mapping quality and within the given insert size range are used to generate the coverage
       across the genome.

       Additionally, regions with repetitive coverage are called, by taking read pairs where at
       least one read of the pair (is mapped and) has mapping quality less than or equal to
       <repetitive max qual>.

OPTIONS

       -noclean
           Use this to not delete the temporary bam file

SEE ALSO

       reapr(1)

                                                                          REAPR-PERFECTFROMBAM(1)