Hello

I have a rather naive question. I ran GATK4 mutect2 on my samples with the following flags:

--contamination-fraction-to-filter 0.0 --max-reads-per-alignment-start 0

The former is to disable downsampling process. So, theoretically I should be able to have equal values in t_depth column (total count of reads per variant) compared to total number of reads aligned on that locus. But they do not match at all.

Any comment would be appreciated. I have no idea what I am missing here.

Thanks