Variant annotation in fishes

Question

[Hayler Edu]

Hello everyone

Today I am analyzing SNP type variants in the species pimelodus yuma. Now what I want to do is use variant effect predictor to check the effect of the found SNPs.

Could someone recommend which predictors I can use in fish?

[Pierre Lindenbaum]

if you have a GTF/GFF3 associated to your fish, you can use almost any classical predictor: VEP, snpeff, bcftools csq etc...