What are SNP effects? in terms of SNPeff output file

Question

[JstRoRR]

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.

Answer 1

[kautilya]

snpEff will add a ANN/EFF entry to the INFO part of your VCF. This indicates the effect a SNP will have on all the listed genes. The effects could be different as in the SNP could be non-synonymous on for one gene while being downstream to another.

Also in case you want to shortlist the most damaging effect you could use GATK VariantAnnotator which would do that for you.

[JstRoRR]

Thanks @kautilya, So that means it has nothing to do with gene overlapping stuff, its just a effect prediction by SNPeff.

[kautilya]

Yes it is a listing of all the effects a SNP will have on the genes and their different transcripts. In some cases there may be an actual gene overlap but that is not the usual scenario.

[JstRoRR]

Thanks for the clarification.