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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

Mutect2 call some structural variants as indel ,how to filter it?

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    Genevieve Brandt (she/her)

    Mutect2 only calls short variants, including SNA and indels. You can find the documentation here. If you want to find structural variants, you can look at this tool documentation here.

    Mutect2 is very sensitive to find all possible variants, and those variants should be filtered using FilterMutectCalls. You can change the parameters when you run FilterMutectCalls to be more or less strict while filtering, and that may help you get the results you expect. 

     

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    zouxuan

    Thank you for you reply.

    As you said 'Mutect2 only calls short variants, including SNA and indels' .In fact ,this variant is not a short variants but a structural variant, so it shouldn't be called out. I had tried  '  -RF NotSupplementaryAlignmentReadFilter' ,but it didn't work. The vcf still exits this variant.Besides, in FilterMutectCalls ,i didn't found some suitable parameters to deal with the problem. 

    Could you give me some suggestions ? Thank you very much.

     

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    Genevieve Brandt (she/her)

    Hi zouxuan, Mutect2 is running as it is supposed to be because this variant is less than 50 bp. In addition, the tool continues to be improved to call larger sites because many people want to find these sites. Filtering is done to filter out artifacts but keep true variants. Since this seems to be a true variant, it would not be filtered out. Hopefully this gives you more insight into what might be happening here. You can also look at the notes on Mutect2 here: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf

    If you have specific variants you do not want in your file, you can use the -XL option (https://gatk.broadinstitute.org/hc/en-us/articles/360045800552-Mutect2) to manually exclude sites.

    Our support team is focused on resolving errors and abnormal results, and it looks like Mutect2 is performing normally in this case. For this question, we cannot guarantee a solution but we ask other community members to help out if they have seen this before. Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools. For context, check out our support policy.

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