I have generated BAM files after mapping my Illumina reads to a reference genome. Now I want to know how much of the reference genome is covered (aligned/mapped) by reads (e.g. 98% of the reference genome is covered by reads). For that I used Bbmap/pileup.sh. It works fast and it is accurate.
However, the 98% I get is the % of nucleotides covered by at least 1 read. It it possible to modify this, and get % of nucleotides that were covered at least with 5 reads?