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

## TL;DR

GRIEVOUS is a command-line tool that simplifies aligning genetic data across datasets to ensure consistency in studies like genome-wide association analyses.

## Contribution

GRIEVOUS introduces a novel command-line tool for resolving genotype inconsistencies across datasets using an internal database and custom indexing.

## Key findings

- GRIEVOUS identifies and aligns biallelic SNPs across summary statistic and genotype files.
- The tool extracts the maximal set of biallelic SNPs common to all datasets after harmonization.
- GRIEVOUS is freely available and can be installed via pip for easy use.

## Abstract

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, GRIEVOUS can also be used to extract the maximal set of biallelic SNPs common to all datasets.

GRIEVOUS and all supporting documentation and tutorials can be found at https://github.com/jvtalwar/GRIEVOUS. It is freely and publicly available under the MIT license and can be installed via pip.