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

Somatic mosaic variants

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    Bhanu Gandham

    HI Laura Collins

    We have not tested Mutect2 for this use case on our end and so we don't have any specifications for Mutect2 for the identification of somatic mosaics. However, we do have collaborators who have used Mutect2 out of the box(without much if any downstream processing) to detect mosaicisim. 

    We are very interested in learning how you are implementing Mutect2 in your analysis and if you are using any specifications. It will be very helpful for the entire GATK community.

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