Picard CollectHsMetrics output

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Giovanni Cerchia

• July 21, 2022 12:29

Hi,

I'm currently using Picard v2.27.4 and I'm calculating HSMetrics over several BAM files. What is not clear for me is how MEAN_TARGET_COVERAGE and MEAN_BAIT_COVERAGE are calculated. For what I know by now, these 2 parameters are obtained by these formulas:

MEAN_TARGET_COVERAGE = ON_TARGET_BASES/TARGET_TERRITORY

MEAN_BAIT_COVERAGE = ON_BAIT_BASES/BAIT_TERRITORY

(In my case TARGET_TERRITORY = BAIT_TERRITORY)

According to the PTC_EXC fields (and subtracting from PF_BASES_ALIGNED the respective excluded bases), it is still not clear how ON_TARGET_BASES and ON_BAIT_BASES are obtained. Can you give me an insight about this part?

Thanks!

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  Genevieve Brandt (she/her)

  • July 21, 2022 19:32

  Thank you for your post, Giovanni Cerchia! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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  Anthony DiCi

  • October 11, 2022 18:38

  Hi Giovanni Cerchia,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  I brought this to our developers for some input and received some feedback. They helped me identify the location in the code where the calculations you reference take place.

  TargetMetricsCollector (Picard) - Line 617

  I hope this helps! If you have any further questions about the CollectHsMetrics tool or any others, please do not hesitate to reach out.

  Best,
  Anthony

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  Anthony DiCi

  • October 19, 2022 12:50

  Hi Giovanni Cerchia,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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