GTQC

GTQC automates quality control and reporting for genotyping array data to evaluate genotype data quality for genome-wide association studies (GWAS).

Key Features:

• Automation of Quality Control Steps: Automates established quality control protocols for genotyping array data to reduce manual QC procedures.
• Comprehensive Quality Metrics: Evaluates a wide spectrum of genotype data quality metrics to assess data integrity prior to downstream analyses.
• Detailed HTML Reporting: Generates HTML reports containing tables and figures that summarize quality control metrics.
• R package implementation: Implemented as an R package for integration into R-based analysis workflows.

Scientific Applications:

• Genome-wide association studies (GWAS): Provides QC and reporting to support data integrity for GWAS.
• Genetic association studies and downstream analyses: Ensures genotype data quality to prevent errors that could compromise study validity.

Methodology:

Implements established genotyping array QC protocols by performing data filtering, outlier detection, and evaluation of genotype quality metrics, and exports summaries as HTML tables and figures.