PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms

This repository contains the complete corpora and PhEval processed TSV results referenced in the study "PhEval: A Framework for Evaluating Phenotype-Driven Variant and Gene Prioritisation Algorithms". The provided materials are integral to the benchmarking process and include:

Phenopacket Corpora:

Phenotype-Only Dataset: Phenopacket store containing phenotypic data without genomic or structural variant information.

Phenotype and Genomic Variant Dataset: Phenopacket store with phenotypic data and associated genomic variants.

Phenotype and Structural Variant Dataset: Structural variant corpus combining phenotypic data with structural variant information.

PhEval TSV Results:

TSV files summarizing the outcomes of nine different benchmarking configurations tested in the paper, including:

Phenotype-Only Tools: Exomiser (phenotype-only mode), Phen2Gene, PhenoGenius, and GADO.

Phenotype and Genomic Variant Tools: Exomiser (with VCF), LIRICAL, and AI-MARRVEL.

Structural Variant Tools: Exomiser and SvAnna.