n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation

mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

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n_alt_count and n_ref_count corrupted at recurrent sites in maf2maf reannotation #317

Open sggaffney opened 2 years ago

sggaffney commented 2 years ago

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.