GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies.

ABSTRACT:

Summary

Harmonizing variant indexing and allele assignments across datasets is crucial for data integrity in cross-dataset studies such as multi-cohort genome-wide association studies, meta-analyses, and the development, validation, and application of polygenic risk scores. Ensuring this indexing and allele consistency is a laborious, time-consuming, and error-prone process requiring a certain degree of computational proficiency. Here, we introduce GRIEVOUS, a command-line tool for cross-dataset variant homogenization. By means of an internal database and a custom indexing methodology, GRIEVOUS identifies, formats, and aligns all biallelic single nucleotide polymorphisms (SNPs) across all summary statistic and genotype files of interest. Upon completion of dataset harmonization, GR

SUBMITTER: Talwar JV 

PROVIDER: S-EPMC11322043 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature