vcf2maf
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n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation
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.