I am wondering about getting the (average) base quality value for the variants called by MuTect2, There were such a column for MuTect v1 output, but not for for MuTect v2?
That's correct, this information is no longer output. Base Quality is taken into account to calculate the genotype likelihoods, so we find the base quality average redundant.
Thank you for your rapid reply, I do not think however that the LOD-scores reflect so well the base quality for that variant, we have samples with variants called by Mutect2 with very low base quality (according to results from MuTect1), around 13-19 and the TLOD can be from 6,3 to at least 40.. I migth want to be able to remove (filter post run) variants that have such low BQ but now my only option is to rerun with a higher treshhold for MBQ? default is 10 (why so low?). Thanks.
Actually I was wrong, that information is still output but in a different form. Have a look at: the QSS annotation.