interpreting SnpEff output

Question

[Alireza]

Hi all.

I ran GATK germline variant discovery on my WES samples.

By running SnpEff on VCF files, many intron variants have been reported.

Why?

Because my sequences are related to exon regions, I expected to see no intron variants in the SnpEFF output.

Answer 1

[Prash]

It could be because of capture method If it were Agilent sureselect Chemistry, V8 + NCV or 5' UTR. Or even the previous versions entails subtle noncoding regions