Thanks for reaching out!
I am not super familiar with the intricacies of the different calling methods and filtering for that TCGA MAF file. I do recall that Mutect2 tends to call more events than other callers (or at least used to):
I imagine that might be one of the reasons, but to get more certainty one would probably need to do a more comprehensive comparison between the MAFs comparing allele frequencies and the differences in types of alterations. Maybe someone else on the mailing list more familiar with this specific file is able to provide a better answer. Glad to hear though that the current GDC MAF is more consistent with what’s in cBioPortal
> Furthermore, do you have any advice on where the best place to obtain updated and accurate mutational info for TCGA-COAD is as this is currently foundational for my PhD project?
I would use the TCGA Pancan data provided here:
You can also use the cBioPortal mutation data, though note that we apply some harmonization (re-annoation thru Genome Nexus), to make the data more suitable for comparison with other mutation data in cBioPortal:
Hope that helps!
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