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?
Please sign in to leave a comment.