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