snpEff predicts stop_gained, but SNP wouldn't produce a stop codon
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9 weeks ago
Nadine • 0

Hi,

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?

screenshot JBrowse Visualization

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,

snpEff wrong prediction stop_gained • 145 views
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Entering edit mode
9 weeks ago

It all depends on the reading frame - there are six reading frames, you need to visualize the feature, where it starts and on which strand it is.

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