README

Quantify bycatch around sites targeted by enrichment.

usage: ./bycatch [-q MINQUAL] [-w WINDOWSIZE] -l loci.bed in.bam

WINDOWSIZE (default=400), sites centered on the target locus are considered.
MINQUAL (default=20), base quality and mapping quality threshold filter.


For each of the target sites in the specified bed file, the following columns
are printed:
CHROM, POS, area, nonzero sites, target depth, max depth, mean, shape.

area - sum of the depth counts for each site in the window around the target
nonzero sites - number sites in the window with nonzero depth counts
target depth - depth count at the target site
max depth - maximum depth count within the window around the target
mean - mean depth count within the window around the target
shape - mean divided by number of nonzero sites; where a low number indicates
	a wider/flatter pileup.