I am trying to find a simple way to generate (post alignment) 1) coverage of reference, 2) depth of coverage - either average or running value accross the genome.
I tried GATK DepthOfCoverage but cant work out the --interval parameter.
samtools bamstats gives coverage
Bases mapped: 1,085,991 (97.8%)
Is there a simple tool that can calculate average depth of coverage and eg min depth max depth