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

Germline false positives in Mutect2

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    Genevieve Brandt

    Thank you for your question! Mutect2 is a popular topic on the forum so we wrote a FAQ article answering many of the questions posted in the last year. Please see that article, as well as our other comprehensive documentation, in case your answer is there.

    Mutect2 has undergone some updates since the version you are using, so I would recommend updating to version 4.1.9.0 and seeing if these issues persist.

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