In some cases BaseCoverageDistribution takes ages to finish. I ran 4 BaseCoverageDistribution commands in parallel, and the smallest sample (by far) still is not finished while the others are. Seems like a bug to me? I will attach a screenshot.
In the output grp file,
#:GATKReport.v1.1:1 #:GATKTable:3:880:%s:%s:%s:; #:GATKTable:BaseCoverageDistribution:A simplified GATK table report Coverage Count Filtered 0 2859049 2932784 1 856997 837791 2 288587 276253 3 95618 91703
what's the meaning of the three columns?