GATK Mutect2 tumor mode
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9 months ago
cocchi.e89 ▴ 150

I am working on some human WGS tumor samples and I want to call somatic variants against the normal tissue sample. I see that Mutect2 had a tumor-mode in previous Mutect2 (now deprecated) guidelines but I can not find it anymore in current GATK Mutect2 guidelines where only PoN are used.

Does it mean that I cannot compare 2 samples directly anymore? Shall I just put the normal tissue in the PoN with other samples? What would be a good way to have a direct comparison between normal and tumor samples (maybe after applying a Panel-of-Normals filter too).

Thank you in advance for any help!

gatk mutect2 tumor human wgs • 593 views
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HI Cocchi,

Although I haven't gone through deeply, I believe you should check out this link where the GATK group described the usage of Mutect2 for a paired t-n tissues. It's updated 14 days ago. Not sure if it serves your WGS data though. https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-

Field

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