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

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    Genevieve Brandt (she/her)

    Hi Tyler Borrman,

    Two sample tumor-only mode should work relatively similarly to one sample tumor-only mode. There are quite a few caveats with running tumor-only mode, it is challenging for Mutect2 to distinguish tumor variants and rare germline variants. This problem won't really be solved with two tumor samples.

    You can search around the forum for other users running Mutect2 with tumor-only mode to find more information as well.

    Best,

    Genevieve

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