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GATK4 Mutect2 tumor only FilterMutectCalls outputted as all germline_risk

ddzhangzzddzhangzz Member
edited August 2018 in Ask the GATK team

I have run GATK4 (v4.0.1.1) Mutect2 for tumor only WGS data and by following, I also ran FilterMutectCalls with most of parameters settings as default such like:

java -Xmx8g -jar gatk-package-4.0.1.1-local.jar FilterMutectCalls \
      -V sample.gatk4.mutect2.vcf
      -O sample.gatk4.mutect2.filtered.vcf

The input vcf has nearly 6 millions mutations but the filtered/annotated output vcf appeared all germline_risk or (clustered_events;germline_risk) without any PASS (from all 10 mice samples). I noticed the TLOD were all much higher than the default --tumor-lod 5.3. I am wondering why no any PASS mutation has been detected?

Also here is a summary for P_GERMLINE

summary(10^pg)
Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
0.6667  0.9995  0.9995  0.9958  0.9995  0.9995

The default cutoff for germline seems 0.025, should i set it even above 0.6667? It seems to high from the default.

Post edited by ddzhangzz on
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