Entering edit mode
6.1 years ago
CY
▴
750
I was trying mutect2 to call somatic variant and found out that, by default, it uses 6.3 as tumor log odds (LOD) filtering cutoff. The formula is:
"Assuming somatic mutations to occur at a rate of ~1 per Mb. Therefore, LOD_T > log_{10} (0.5 \times 10^{-6} ) \approx 6.3 $$, which guarantees that our false positive rate, due to noise in the tumor, is less than half of the somatic mutation rate"
Here is the GATK link https://gatkforums.broadinstitute.org/gatk/discussion/4463/how-mutect-identifies-candidate-somatic-mutations
It seems to me the tumor mutation frequency is too arbitrary. The mutation frequency varies between different cancer type by two magnitude.
Does this make sense? Or I misunderstood it?
