Dataset for testing the calibration of the variant prediction methods

Dataset used for testing the calibration of 6 methods for predicting the impact of single nucleotide variants in the publication: 

Benevenuta S, Capriotti E, Fariselli P. (2021). Calibrating variant-scoring methods for clinical decision making. Bioinformatics. DOI: 10.1093/bioinformatics/btaa943.

The file contains the following columns:

CHROM: Chromosome number  

POS: Chromosome coordinate

REF: Reference Allele     

ALT: Alternative Allele     

Coding: Coding Variants (Yes/No) 

Effect: Variant impact (Pathogenic/Benign) 

DANN: DANN output   

PhDSNP: PhD-SNPg output 

FATHMM: FATHMM output 

CADD: CADD output   

DeepSea: DeepSea output

Eigen: Eigen output