Mutect2 low allele fraction mutation calling

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TA

• September 22, 2022 18:18

Hi,

I have two questions on low fraction mutations:

Question 1:

I wanted to know if Mutect2 had been validated on calling extremely low fraction VAF mutations (as can be found in ctDNA). Are there particular settings you can use for extremely low VAF mutation detection?

I saw here (https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2) a link where there was suppose to be a blog post for low fraction mutation detection but it still has not been completed - is this blog somewhere else?

I also saw here (https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2019-03-05-New!_Mitochondrial_Analysis_with_Mutect2.md?id=23598)  that in the mitochondria mode it can call low fraction mutations but it says that you are not confident in calls below 5% at the bottom of the document.

Question 2:

If I use the force-call-filtered-alleles call at a particular site, and this site has 1 ALT allele and 1999 REF alleles, will it output a VCF with a count of this 1 ALT allele? Or does the force-call-filtered alleles command not output ALT allele counts at a given site if they are extremely rare?

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  Genevieve Brandt (she/her)

  • September 22, 2022 23:05

  Thank you for your post, TA! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

  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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