Question: GATK Mutect2 tumor mode
1
gravatar for cocchi.e89
6 weeks ago by
cocchi.e89110
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. https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-

Field

ADD REPLYlink written 15 days ago by field65410
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2006 users visited in the last hour