I have performed some mutect2 (v 18.104.22.168) variant callings using the following command line:
gatk Mutect2 -R "$reference" \
--tumor-sample $tumour1ID --normal-sample $normalID --input $tumour1Bam --input $tumour2Bam --input $normalBam -germline-resource "$germlineResource" \
--f1r2-tar-gz "$outputf1r2" --output $out
gatk LearnReadOrientationModel -I "$outDir"/mutect2.f1r2.tar.gz -O "$out1"
gatk FilterMutectCalls -V "$outDir"/mutect2.raw.vcf -R "$reference" \
--contamination-table "$contTable1" --contamination-table "$contTable2" --ob-priors "$orientModel" -O $out2
I was wondering if the distributions of VAFs that I am getting are okay. The first image comes from a different cohort than the second:
I am aware that mutect detects just somatic mutations, but I would expect also some somatic variants with higher VAFs (which at least in the second image are just a few). Do you think that those distributions are okay or that I should expect something like in the following case?
Do you think if there is some reason which could be avoiding the detection of somatic variants with high VAFs (>0.4)?
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