Genome Analysis Toolkit

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

VAF distribution of Mutect2 tumour-normal matched calling

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    Genevieve Brandt (she/her)

    Hi Jenifer

    I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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    Pamela Bretscher

    Hi Jenifer,

    Looking at the distributions, nothing seems especially off. The first distribution definitely looks reasonable. The second image would definitely be an expected result if this is from a sample with low purity which can result in very low variant allele fractions (like a blood sample). Do you have more information about the biological context of these samples? 

    Kind regards,

    Pamela

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    Jenifer

    Okay thanks! Both cohorts are solid tumour samples, but I don't know their purity. I just wanted to be sure that this can be normal and not caused by mutect2 avoiding to call variants with high VAFs.

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    Pamela Bretscher

    Hi Jenifer,

    Yes, both distributions can definitely be normal. I don't think there are any issues with Mutect2 going on here and it most likely is just related to the purity of the samples!

    Kind regards,

    Pamela

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