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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

How to run muTect without normal sample?



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    Anthony DiCi

    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. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Anthony DiCi

    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.gz

    That 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.


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    Yingjie Zhu

    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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