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

How do I set less stringent germline filtering in Mutect2 / filtermutectcalls, many false negatives


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    Genevieve Brandt (she/her)

    Hi Tjitske de Vries,

    Tumor-only calling is very challenging when it comes to variant filtering. Having lenient germline filters will end up with a high percentage of sites in the output being germline sites. However, like you said, having more stringent germline filtering can throw out real sites. 

    You can use the option --f-score-beta in FilterMutectCalls to adjust the balance of the germline filters. We don't have a lot of documentation yet on how to adjust this parameter so if you find any improvements, please post here since it might be helpful for other users running tumor-only calling. The only note is that it cannot be negative.

    Hope this helps!


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