GATK4 Mutect2 tumor only FilterMutectCalls outputted as all germline_risk
I have run GATK4 (v126.96.36.199) 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-188.8.131.52-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.