frip provides extremely basic functionality for calculating the fraction of reads in an experiment falling into peaks.
Keep in mind that I whipped this up very quickly for a specific case, so I can't guarantee it isn't filled with bugs.
You only need to provide a bam file (cram and sam soon to come) and a bed file. The bam doesn't need to be indexed. The result is written to stdout.
frip a.bam a.bed > a.txtNote that for now the bed file must be in full 6 column format - providing an invalid bed will silently produce a frip score of 0.0. The most common reason for an invalid bed is 3 column formatting. I have plans to handle 3 column beds but for now something like this will do the trick:
awk '{$4=".";$5="0";$6="+"}1' original.bed | tr ' ' \\t > fixed.bed