What it does

This tool takes an MAF file and an interval file and relates coverage information by interval for each species. If a column does not exist in the reference genome, it is not included in the output.

Consider the interval: "chrX 1000 1100 myInterval" Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this:

chrX 1000 1100 myInterval H XXX YYY

chrX 1000 1100 myInterval M XXX YYY

chrX 1000 1100 myInterval R XXX YYY

where XXX and YYY are:

XXX = number of nucleotides

YYY = number of gaps

Alternatively, you can request only summary information for a set of intervals:

#species	nucleotides	coverage
hg18	30639	0.2372
rheMac2	7524	0.0582
panTro2	30390	0.2353

where coverage is the number of nucleotides divided by the total length of the intervals provided in the BED file.