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Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

[GATK4 beta] no filter-passing variants in Mutect2 tumor-only runs using default parameters

dayzcooldayzcool Member
edited August 13 in Ask the GATK team

Hello,

I would like to ask your advice on the tumor only mode of Mutect.
I ran GATK4 beta.3's Mutect on 20 tumor samples using tumor-only mode, and found no variant passing filters. Every variant is filtered out after running FilterMutectCalls tool. It seems that germline risk is estimated very high overall.
Mutect2 was executed using the scripts/mutect2_wdl/mutect2_multi_sample.wdl in the GATK source repository. gnomAD is given for the population af source and default parameters are used.
I'd appreciate it if you would help run tumor-only mode of Mutect.

FYI, 10^P_GERMLINE (log10 posterior probability for alt allele to be germline variants in INFO) of a tumor sample distributes as below. Outliers are not plotted for the sake of simplicity.

Summary(10^P_GERMLINE)

Min. 1st Qu. Median Mean 3rd Qu. Max.
0.04699 0.93345 0.99919 0.94155 1.00000 1.00000

P_GERMLINE plot

(Additionally, no toolbar button works on this 'ask a question' page I am writing this question. (such as bold, italic, file upload buttons) Is it just me?)

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