The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks (  ) each to make a code block as demonstrated here.

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

Member
edited August 13

Hello,

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?)