I've been using HSMetrics for a while to get 2X/10X/20X/30X coverage, as well as average probe and target coverage.
I've noticed lately that the 2X/10X/20X/30X numbers start to skew lower for alignments with high duplicate levels. In fact, if I run MarkDuplicates and then re-run HSMetrics, the 2X/10X/20X/30X numbers actually increase, which seems counterintuitive. On top of that, coverage counts that I generate using BEDTools coverageBed don't match the 2X/10X/20X/30X numbers or the average target coverage depth counts I get from HSMetrics.
I've searched high and low and not seen a good explanation of the inner workings of HSMetrics. Is it applying some of its own filtering? Is it perhaps sampling only a portion of the data?
My next steps are to try both HSMetrics and BEDTools with a small target set to see if I can replicate and explain the behavior. After that, I guess I'll try to walk through the Picard code.
But if someone out there knows what might be going on, I'm all ears.
I've noticed lately that the 2X/10X/20X/30X numbers start to skew lower for alignments with high duplicate levels. In fact, if I run MarkDuplicates and then re-run HSMetrics, the 2X/10X/20X/30X numbers actually increase, which seems counterintuitive. On top of that, coverage counts that I generate using BEDTools coverageBed don't match the 2X/10X/20X/30X numbers or the average target coverage depth counts I get from HSMetrics.
I've searched high and low and not seen a good explanation of the inner workings of HSMetrics. Is it applying some of its own filtering? Is it perhaps sampling only a portion of the data?
My next steps are to try both HSMetrics and BEDTools with a small target set to see if I can replicate and explain the behavior. After that, I guess I'll try to walk through the Picard code.
But if someone out there knows what might be going on, I'm all ears.
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