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 using a tumor as "pseudonormal" and relapsed as "tumor", PON necessary?

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    Gökalp Çelik

    You can use pseudonormal as normal in a Tumor-Matched Normal study as indicated in the documentation. PON for Mutect2 is not something that you think it is actually. It is a collection of artifacts generated by our team to filter out sequencing artifacts from tumor sequencing data and preparation of this PON can be very tricky unless you know your way through. If you are using human samples we definitely recommend using the PoN that we provide for Mutect2. For others you may try to generate but your mileage may vary. Also since you have a matched normal this may not be ultimately necessary for your purpose. 

    I hope this helps.

     

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    Jaime Alvarez Benayas

    Thank you, it did help!

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