Hi I am calling SNP/Variants from RAN-Seq data. I have followed the GATK pipeline for RNASeq and annotated the final vcf file using SNPeff. Now in the final vcf file, resulted from SNPeff, I see some additional information in the form of effects. How can I define these effects, are these effects a direct result of genes overlapping (for an individual position it would give me multiple calls in the annotation INFO column) or its just a prediction that particular SNP at particular genomic location affects all the listed genes in one way or another?
Thanks for any suggestion.