alt_allele_in_normal vs normal LOD: Is alt_allele_in_normal redundant?
As far as I understand, normal LOD applies baeysian model to test whether normal sample carries the variant allele. However, the VCF also tag the entries as 'alt_allele_in_normal' if variant allele appears in normal sample. Does this 'alt_allele_in_normal' redundant? More importantly, does it make sense to filter the entries as soon as the normal contains a few variant reads especially when sequencing depth is high?
Cheng Yan alt_allele_in_normal is a filter from an old version of Mutect2. Only the probabilistic normal artifact model remains.
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