How to run muTect without normal sample?
AnsweredI have bam files from single cell, I wonder to know is that possible to run muTect without matched normal? So I can call all mutations in a bam file.
Thank you!
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Thank you for your post, Yingjie Zhu ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
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Hi Yingjie Zhu,
Thank you for writing to the GATK forum! I hope that we can help you sort this out.
In short, it is possible to run Mutect2 without a matched normal. As you can see in the example below, when you input the normal BAM file, you specify the normal to Mutect2 with the -normal normal_sample_name argument. To run Mutect2 without a matched normal, you do not add the -normal argument. It will run without a normal if you do not tell the tool what the normal is.
gatk Mutect2 \
-R reference.fa \
-I tumor.bam \
-I normal.bam \
-normal normal_sample_name \
--germline-resource af-only-gnomad.vcf.gz \
--panel-of-normals pon.vcf.gz \
-O somatic.vcf.gzThat said, we do not recommend running the tool without a matched normal. Running without a normal will adversely affect your results. Specifically, even extremely rare germline mutations are more common than somatic mutations. So if you do not specify a normal, your call will be full of rare germline mutations that you can’t distinguish from the somatic mutations you are trying to identify.
I hope this helps provide some clarity! Please do not hesitate to reach out if you have any other questions in the future.
Best,
Anthony -
Thank you explaining me how to run Mutect2 without normal. Since I am using it in single cell mutation calling, I want to call every mutation whatever germline or somatic mutations, so that's why I want to run Mutect / Mutect2 without normal. I appreciate your explanation here.
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