over targeted regions in a genome
snp_reports -v
snp_reports -q $snp_table $target_bed $coding_gtf $depth_summary $out_snp_summary_table
This tool reports several statistics describing the rate of protein coding SNP calls from a next-gen sequencing analysis such as an exome capture.
These results can be used to assess the quality of the SNP caller used, filtering thresholds, etc. Location with less than 10 fold coverage, and
variants with caveat are ignored.