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GATK3 MuTect2 homologous mapping filter & events

jmoajmoa koreaMember
edited July 19 in Ask the GATK team

Hi, I'm using GATK3 MuTect2 to call Somatic variants and encountered filter called "clustered_events" and "homolougous_mapping_events".

By reading this thread i got some idea what "clustered_events" is.

As for "homologous_mapping_events" I've encountered this thread but couldn't catch the meanings.

Is variants marked as "homologous_mapping_events" when there are more than 3 events(SNV, Indels) in a single read(assembled haplotypes by MuTect2)?

And, am i correct with the interpretation of "events" as SNVs and Indels?

Thanks.

Post edited by bshifaw on

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited July 19

    Is variants marked as "homologous_mapping_events" when there are more than 3 events(SNV, Indels) in a single read(assembled haplotypes by MuTect2)?
    And, am i correct with the interpretation of "events" as SNVs and Indels?

    Yes, 3 or more mutations that are found on a haplotype. It's a filter that detects homologous sequences and filters out variants falling into sequences that have three or more events observed in the tumor. pub link. Mutect2 will add the homologous_mapping_event filter if the eventcount is 3 or more. eventcount being the number of events in the haplotype. source code link

    You may want to switch over to GATK4, as GATK 3 is no longer supported.

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