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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

Filtering Mutect output from FFPE based targeted panel sequencing data



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    Genevieve Brandt (she/her)

    Hi Maxwell Douglas,

    It is challenging to detect true variants when you are running tumor-only mode with FFPE data. You are dealing with two challenges that do not help FilterMutectCalls to succeed. I would expect that many of your variants are false positives, but also that FilterMutectCalls will have a hard time determining which are false positives and which are true positives. 

    We are continuing to improve Mutect2 so in the future you may find more success, but right now it looks like you are running the commands correctly, you are just up against a challenging data set. You can read more in this comment from David Benjamin, one of our Mutect2 developer leads:

    Let me know if you have any further questions.

    Best regards,


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    Genevieve Brandt (she/her)

    Hi Maxwell,

    We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

    Kind regards,


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