What it does
This tool takes a 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.
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 provided intervals.