gene function in refgene when using annovar

Question

[897598644]

Excuse me:

My NGS data is whole exome sequencing data. After calling variants, I annotated variants with refGene using annovar. In the column 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!

Answer 1

[Kizuna]

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.

[897598644]

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