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

Mutect2 with and without UMI information


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    Genevieve Brandt (she/her)

    Hi Davy Deng,

    This statement is just regarding running GATK with amplicon data. HaplotypeCaller and Mutect2 do not use UMIs, but if you have UMIs, we recommend running the UMI aware MarkDuplicates step. If you have amplicon data and do not have UMIs, you have to skip MarkDuplicates.

    Hope this helps!


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