Question: picard Hs metrics and MarkDuplicates
gravatar for User6891
4.2 years ago by
User6891250 wrote:

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?


picard • 2.1k views
ADD COMMENTlink modified 4.2 years ago by Dan D6.8k • written 4.2 years ago by User6891250
gravatar for Dan D
4.2 years ago by
Dan D6.8k
Dan D6.8k wrote:

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.

ADD COMMENTlink written 4.2 years ago by Dan D6.8k
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