SNPEff - Exonic Variants

Question

[hoollyywood]

Hi folks

Is there a simple way to identify all exonic variants in SNPEff results in the same way that wAnnovar results can be filtered on the Func.RefGene column for "exonic"?

Is my only option to identify and aggregate the different variant types in the ANN= part of the INFO field?

I can't help but think there must be a more straightforward method?

TIA

Answer 1

[Jeremy Leipzig]

what do you get with the options -no-intergenic -no-intron ?

Answer 2

[Jimmy]

There’s a few ways you can isolate SNPs only in exons.

I’m not familiar with SNPEff but here’s a different one. You must have a BED/GFF/GTF file with the coordinates of features in the genome, including exons. You want to take this and end up with a file containing coordinated only coordinates of the exons. To do this, you could probably use awk to grab features whose value in the feature column corresponds to “exon” and redirect these sites into a new file. So now you have a BED/GFF/GTF containing only exonic coordinates.

I imagine you have a VCF file. You can use BEDtools (a command-line utility) to find the intersect between your exon-coordinates file and your VCF. You can end up with a file containing only VCF sites that fall within the exons. If you know Python, pybedtools (a Python wrapper around BEDtools) can also be used for this. From here it should be straight forward to filter for SNPs in your exon-only VCF.