Recent changes to the terms used in the G2P database are aligned with global standards, but are not compatible with old versions of the VEP G2P plugin. We’ve updated the latest version of the VEP G2P plugin (Ensembl 105) to be compatible with both the old and new formats.Continue reading
A common use case for the VEP is as a first step towards identifying the causal genetic variant of a rare phenotype from whole genome/exome sequencing. The VEP tells you which genes are hit, what effects they have on them, and you have to begin the long laborious process of filtering those down. Things you might consider include allele frequency, association with genes known to be involved in rare disease and whether both genes in a diploid organism are affected. Rather than faffing about doing this manually, you can use the G2P (genotype to phenotype) plugin instead, which was recently published as a preprint.