How does picard CollectWGSmetrics estimate coverage on Soft-Clipped Reads?

Question

[knagul]

Does picard CollectWGSMetrics take into account soft-clipped reads to estimate mean coverage? Aligner used is bwa-mem.

Answer 1

[Dan D]

The tool works by iterating over the provided reference and counting the number of read bases mapped to each reference base. The soft-clipped bases would be ignored in the total count because they wouldn't align to a given reference base. The other, non-clipped bases would be included in the total unless they were excluded for some other reason (mate overlap, no mate, duplicate read, etc).

So soft-clipped reads will be evaluated. Soft-clipped bases will be omitted from the counts.