Warnings

Warnings

Here are a few things to keep in mind when using TAPES

ACMG classification and Pathogenicity prediction

The ACMG criteria and classification (from Benign to Pathogenic or class 1 to 5) reflect the PROBABILITY of a variant to be pathogenic. A variant of class 4 (Likely Pathogenic) is NOT MORE pathogenic than a variant of class 5 (Pathogenic). Instead, it is just MORE LIKELY to be pathogenic.

The same goes with the ACMG criteria modeling from Tavtigian et al that TAPES uses.

This has implications in the --by_gene score used in TAPES. This score is the sum of all probabilities multiplied by the number of sample affected. It reflect the probability of the genes to be affected by a pathogenic variant in the cohort.