performance of indel calling by MuTect2
AnsweredI'm interested in MuTect2 performance on indel calling. My experience in using MuTect2 in some research projects of mine is that the indel accuracy is a bit low, and a lot of the indels are false positives. I wonder what's your thoughts on that? Any recommendations about how to increase the indel calling accuracy?
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Hi huan wang,
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I'm also observing a rather abnormally high number of indels with Mutect2, specifically insertions. When comparing to a group of previously generated VCF files using the same data a couple years ago, I don't see as many indels present. I didn't examine it closer, but I assumed that it was due to the different GATK versions and flags utilized in the workflow.
GATK version - v4.1.4.1
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We recently have made updates to Mutect2 so I would recommend first, use the most recent version. There is also a lot of information about Mutect2 on this forum, so please see other posts for more information. Here are documents about Mutect2 and how to troubleshoot the output (Some of the documents are why variants are not called, but they still have helpful info):
- When HaplotypeCaller and Mutect2 do not call an expected variant
- FAQ for Mutect2
- Expected variant at a specific site was not called
If you cannot find an explanation after doing more examination, please make a thorough post with examples so that we can look into it.
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