Hi. I have identified and annotated several variants by ANNOVAR. Which tools can be used to determine if the variant was in the last exon or last 50 bases of the penultimate exons.
I don't know about ANNOVAR but VEP can give you the exon number which will appear as something like 1/12, 5/8 etc. You could filter your data to only get those where the two numbers are the same, which would give you the last exon. You can also get the penultimate exon by filtering for those where the first number is one less than the second, but identifying the position in the exon may take some custom scripts.
Are you trying to predict NMD escape? We are working on a plugin for that.
There is the existing Nearest Exon Junction Boundary plugin, which can tell you how far the variant is from the start/end of an exon, so you could filter in this too.
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version 2.3.6
Thank you! I'll re-annotate the variant using VEP. BTW, is the plugin accessible now?
We hope it will be out with the next Ensembl release.
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