picard Hs metrics and MarkDuplicates

Question

[User6891]

Does anyone know if reads, that are marked as duplicates by Picard MarkDuplicates.jar, are taken into account when calculating metrics like 'on bait' or 'on target' coverage in Picard CalculateHsMetrics.jar?

Answer 1

[Dan D]

Yes, they are. If you look at the HSMetricCollector class, it's using the PF_UQ_BASES_ALIGNED property from the TargetMetricsCollector class when calculating the on-target percentage. That property does not include reads marked as duplicate.