SNPEff calling all intragenic SNPs as frame shifts

[tgarcia]

I'm working with a colleague of mine to compare the genomes of two intra-generic vertebrate speceis. We're interested in identifying genome-wide differences and at the moment are looking at the effects of single nucleotide and multi nucleotide differences in genes. We've identified variants by making a whole genome alignment and saving the variants in a vcf file. Our problem is that when we try to annotate the vcf file with SNPEff all the single nucleotide differences within gene boundaries are labeled as FRAME_SHIFT which makes no sense.

Has anyone else run into this issue?

[cariboudoug]

I haven't come across this issue... My first thought was that it could be an annotation problem, but I'm not sure.
It might be useful to post an example line of SnpEff output.

[tgarcia]

Thanks for your reply! It turns out the issue was an older version of VarScan. We updated to the latest VarScan (2.3.6) and that resolved the issue.