Mutect2 merge stats

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Saskia

• March 29, 2021 15:05

Hi there,

b) What does merge stats mean?

I am running Mutect2 on several hundreds samples and am unsure what the step merge stats actually does.

Do I only have to run it when I scattered samples before running Mutect2 or do I have to run it in in any case as like a population cross check? As in when calling somatic mutations in many samples will it discard calls that have been made in more than one sample as it would be unlikely to be a somatic mutation?

cheers

saskia

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  Genevieve Brandt (she/her)

  • March 30, 2021 18:24

  Hi Saskia,

  I am going to move your post into our Community Discussions -> Documentation Questions topic, as the Somatic topic is for reporting bugs and issues with GATK.

  You can read more about our forum guidelines and the topics here: Forum Guidelines.

  Best,

  Genevieve

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  Genevieve Brandt (she/her)

  • April 16, 2021 19:02

  Hi Saskia,

  MergeMutectStats is only necessary if you ran Mutect2 scattered. It's a way to combine the stats files across these scatters, not for a population cross-check. 

  There are details in this Mutect2 tutorial:

  However, if you are running on a cluster or the cloud you need to keep track of the stats file. For example, you need to delocalize it from a VM, as is done in the Mutect2 WDL. You can explicitly input the stats file with the -stats argument in FilterMutectCalls. If you are scattering Mutect2 over multiple nodes you must merge the stats files with MergeMutectStats and pass merged.stats to FilterMutectCalls.

  Hope this helps!

  Genevieve

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