I did a variant analysis with gatk and used snpEff to annotate the variants. On one position snpEff annotates the effect as stop_gained. But when I visualize this position there is no new stop codon due to the variant. What could the reason for this be?
Only way I could see a new stop would be the opposite strand combined with a reading frame shift making it a TAG. Could this be the reason for this prediction?
Thanks for any help, Best,