Hi, I am attempting to identify the exon that each of my synonymous or missense SNPs in the 1000 genomes data belongs to. I am using the GENCODE GTF files found here: https://www.gencodegenes.org/human/ and extracting all exons.
I then use bedtools to identify which exon each of my SNPs fall in. It appears that many of my SNPs' co-ordinates are not within any exon. What I would like to know is if and how synonymous or missense SNPs can fall in intronic regions?