I have generated single vcf for 2 samples. Then annotated the vcf file using snpEff and I extracted only variants for gene "GLA".
In my case for the below two variants, there are more than one annotation. Multiple annotations are separated by comma.
1) Why am I getting multiple annotation for one variant?
I am interested in extracting only exonic variants. Mutations in exon regions will affect the protein by either creating missense and nonsense mutations. As per the below summary, I have variants from exon "73,274". I believe, non_coding_exon_variant and non_coding_transcript_variants are also included in 73,274.
Why the non_coding variants are clubbed with exons?