snpQT

snpQT performs comprehensive quality control and imputation on human genomic data to standardize genotypes, remove artefacts and population outliers, convert human genome builds, and produce data suitable for downstream analyses such as genome-wide association studies (GWAS).

Key Features:

• Comprehensive Quality Control: Implements approximately 36 discrete quality filters and correction steps within a standardized pipeline.
• Graphical Reporting: Generates detailed graphical reports illustrating data states before and after each QC procedure.
• Human Genome Build Conversion: Supports conversion between different human genome builds.
• Population Stratification and Outlier Removal: Performs automated population stratification against the 1,000 Genomes Project and facilitates removal of population outliers.
• Built-in Imputation: Provides integrated imputation with pre- and post-imputation quality controls.
• Modular Pipeline Architecture: Organizes QC steps into modular, composable workflows.
• Reproducibility and Scalability: Uses Nextflow and BioContainers to enable reproducible execution across computational environments.

Scientific Applications:

• Genome-wide association studies (GWAS): Produces QCed and imputed genotype datasets to improve reliability of association analyses between genetic variants and phenotypic traits.
• General genomic research: Provides standardized QC, population stratification, build conversion, and imputation for downstream genetic and population-genetic analyses.

Methodology:

Implements a modular Nextflow pipeline using BioContainers; executes ~36 QC filters and correction steps, automated population stratification against the 1,000 Genomes Project with outlier removal, human genome build conversion, integrated imputation with pre- and post-imputation QC, and generation of graphical QC reports.