Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2 merge stats

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    Genevieve Brandt (she/her)

    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)

    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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