Variant effect predictor in ictalurus punctatus

Question

[Hayler Edu]

Hello everyone

I performed a VEP analysis today using a catfish reference genome and my VCFs are from the species Pimmelodus Yuma. The problem is that the predictors did not give me any results in the missense variants. Is this normal?

Here are the pictures

[barslmn]

I think VEP uses precalculated values for most of these tools and I don't think they are precalculated for your organism.

[Hayler Edu]

Thanks! Do you think that is better to use each predictor in the UNIX terminal?

[barslmn]

I never tried building one of these myself, so I don't know about the computational requirements nor if it's achievable for other organisms (since some tools are derivative) with most of these tools. However, SIFT looks promising. https://www.ensembl.org/info/genome/variation/prediction/protein_function.html#sift