I've noticed in my last two runs of maf2maf that n_alt_count and n_ref_count can be altered during reannotation by maf2maf.pl. This occurs when a variant is present in multiple samples. For these recurrent variants, the values of n_alt_count and n_ref_count can be erroneously copied from one sample to another. Apologies for not having generated a minimal reproducible example at this time, but I wanted to share asap.
I've noticed in my last two runs of maf2maf that
n_alt_countandn_ref_countcan be altered during reannotation bymaf2maf.pl. This occurs when a variant is present in multiple samples. For these recurrent variants, the values ofn_alt_countandn_ref_countcan be erroneously copied from one sample to another. Apologies for not having generated a minimal reproducible example at this time, but I wanted to share asap.