Running Mutect 2 with matched normal vs tumor mode
So I've finished running my analysis for Mutect 2. My main question is this. When I ran this analysis Mutect found lets say 250 possible mutations in my tumor with pair normal. However when I run the same with just the tumor sample I get considerable more mutations. Its in the 7600s. Is this normal or am I doing something wrong? The way the final analysis is set up is the vcf is displayed when the chr that is mutated in at least two or more samples.
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If you could also confirm for me the default read depth that Mutect2 does. I've read somewhere that its 50 but I would like confirmation. Thanks!
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Hi Mommy Misato,
The result you are seeing is expected because when you do not have a matched normal sample, Mutect2 will call all germline variants in addition to somatic variants. You can find more information about the differences between tumor-only and matched-normal mode in the Mutect2 FAQ. As for your second question, I am not sure what value you are referring to as Mutect2 accommodates a wide range of read depths. You can find information about the default values for various parameters in Mutect2 in the tool documentation. I am going to move your post to the General Discussion topic as the Somatic topic is for reporting bugs with GATK.
Kind regards,
Pamela
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Thank you!
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