Mutect2 using a tumor as "pseudonormal" and relapsed as "tumor", PON necessary?
Hello:
I have seen that it is possible to use Mutect2 using a tumor as "pseudonormal" and relapsed as "tumor" (#6 on this page: https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-for-Mutect2). However, I am unsure as if I should use a Panel of Normals and whether this panel should be generated with healthy individuals.
Thank you.
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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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Thank you, it did help!
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