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Fields in the Genome-Phenome Analyzer

Variant file effect terms recognized

Effect terms that are recognized are listed at this link, though each group typically uses only a few of these, such as the core terms missense, frameshift, and synonymous.  The listing here is periodically updated to include all SnpEff effect prediction terms, but let us know if we are missing any.  The terms are case-insensitive.  If multiple terms are used (separated by "|" or "&" or "," or "/"), each effect term is considered and the one with the highest severity is chosen.