How does picard CollectWGSmetrics estimate coverage on Soft-Clipped Reads?
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4.8 years ago
knagul ▴ 10

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

coverage WGS • 1.5k views
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4.8 years ago
Dan D 7.3k

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.

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