Picard collectmultiplemetrics (CollectQualityYieldMetrics and CollectInsertSizeMetrics) count soft clipped bases and mark duplicate reads

Question

[kani]

Picard tool collectmultiplemetrics (CollectQualityYieldMetrics) exclude the soft clipped bases and mark duplicate reads to calculate the percentage of PF Q30 bases?

Answer 1

[Pierre Lindenbaum]

https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/analysis/CollectQualityYieldMetrics.java#L165

i don't see markedup are excluded here. (but may be elsewhere ?)

https://github.com/broadinstitute/picard/blob/master/src/main/java/picard/analysis/CollectQualityYieldMetrics.java#L184

the whole read is used.

[kani]

Thanks Pierre Lindenbaum.

Wonder why CollectQualityYieldMetrics not exclude mark duplicate reads and clipped bases by default to evaluate the read quality (eg.PF Q30), like CollectInsertSizeMetrics which has an option to include marked duplicates by default not counted.