GRIEVOUS

GRIEVOUS harmonizes variant indexing and allele assignments across datasets to resolve cross-dataset genotype inconsistencies.

Key Features:

• Cross-dataset variant homogenization: GRIEVOUS identifies, formats, and aligns all biallelic single nucleotide polymorphisms across all summary statistic and genotype files of interest.
• Internal database and custom indexing: GRIEVOUS employs an internal database and a custom indexing methodology to enable variant harmonization.
• Common SNP extraction: Upon completion of dataset harmonization, GRIEVOUS can extract the maximal set of biallelic SNPs common to all datasets.

Scientific Applications:

• Multi-cohort genome-wide association studies: GRIEVOUS ensures data integrity by harmonizing variant indexing and allele assignments across datasets for cross-cohort analyses.
• Meta-analyses: GRIEVOUS resolves genotype inconsistencies to enable valid statistical combination of results from multiple studies.
• Polygenic risk score development, validation, and application: GRIEVOUS harmonizes variant data to support consistent genotype information across training and target datasets for polygenic risk score workflows.

Methodology:

GRIEVOUS uses an internal database and a custom indexing methodology to identify, format, and align biallelic SNPs across datasets.