I am working on functional annotation of my exome-chip variants.
I am not sure what are the differences using annotation from (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE).
ANNOVAR annotates all SNPs using refseq’s sequence information without using any algorithm.
(SIFT, Polyphen, PROVEAN) annotates all SNPs using certain algorithms.
LOFTEE is specific for annotating LoF variants, and (SIFT, Polyphen, PROVEAN) also predict deleterious/disruptive variants.
I guess there is no classical answer to categorize LoF variants, but I would like to know what would be the main differences using those software?