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gene function in refgene when using annovar
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4.0 years ago
897598644 • 80
China

Excuse me:

My NGS data is whole exome sequencing data. After calling variants, i annotated variants with refGene using annovar. In the column of Func.refGene, there were many filter options like:exonic
splicing
ncRNA
UTR5
UTR3
intronic
upstream
downstream
intergenic
exonic;splicing
ncRNA_exonic
ncRNA_UTR3
ncRNA_UTR5

So how can i select from them?

Thanks in advance!

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3.1 years ago
Kizuna • 780
France, Paris

in Whole Exome Sequencing you need to focus on the coding variants such as : nonsense, missense, splice site variants (ranging between +5 and -5 of the exon boundary).. In addition, you should work with Indels, mainly frame shift InDels.

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But the reagent also capture UTR5' and UTR3'. What else should i focus on? and How should i know whetehr the splice site was in the scale between +5 and -5 of the exon boundary.

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