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

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sggaffney opened this issue Jun 2, 2022 · 0 comments

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@sggaffney
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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.

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