Question: GATK Mutect2 tumor mode
gravatar for cocchi.e89
6 weeks ago by
cocchi.e89110 wrote:

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 human mutect2 tumor wgs • 139 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by cocchi.e89110

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.


ADD REPLYlink written 15 days ago by field65410
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