Currently, alignment coverage is compute for a whole input file but, sometimes users want to compute the coverage for a given region or set of regions. A region filter parameter should be added to the alignment depth command line:
-r, --region STRING Coverage for a comma separated list of regions, e.g.: 1:300000-400000000,15:343453463-8787665654 [null]
--region-file STRING Coverage for a list of regions stored in a file, one region per line, e.g.: 1:6700000-560000000 [null]
Currently, alignment coverage is compute for a whole input file but, sometimes users want to compute the coverage for a given region or set of regions. A region filter parameter should be added to the alignment depth command line:
./build/bin/hpg-bigdata-local.sh alignment depth -i -o [-r,--region chrom1:start1-end1,chrom2:start2-end2,...] [--region-file region_filename]