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 tumor-only mode without normal match or germline resources

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    Gökalp Çelik

    Hi Leo

    Short answer: No. 

    Mutect2 uses a different model compared to HaplotypeCaller when calling variants and not using any PoN, germline resource or a matched normal will make Mutect2 to push more false positive calls to PASS filters after FilterMutectCalls step. Mutect2 is more naive and will almost call any different looking site as a variant as opposed to HaplotypeCaller which uses a germline model as a prior for calling variants. 

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