snpQC

snpQC performs R-based preprocessing, quality control, filtering, and storage of genotypic data from Illumina SNP arrays to ensure reliable datasets for genome-wide association studies (GWAS) and genomic prediction.

Key Features:

• R-based implementation: Implemented as an R pipeline for processing Illumina SNP array genotypic data.
• Automated quality control: Applies a comprehensive set of QC metrics to Illumina SNP array data with user-definable filtering thresholds.
• Comprehensive reporting and filtering: Generates detailed QC reports and produces filtered datasets including a genomic relationship matrix.
• Data integrity and long-term storage: Constructs a database to store genotypic, phenotypic, and quality metrics to maintain dataset consistency as new samples are integrated.
• High-throughput compatibility: Designed for integration into high-throughput genotyping environments for large-scale studies.
• Cross-species and array design flexibility: Supports multiple species and array designs for diverse genotyping contexts.

Scientific Applications:

• Genome-wide association studies (GWAS): Ensures high-quality genotype data for identifying genetic associations with traits.
• Genomic prediction and breeding value estimation: Produces filtered datasets and genomic relationship matrices used in genomic prediction and estimation of genomic breeding values.
• Longitudinal studies and breeding programs: Enables integration of new samples over time for ongoing genotyping in longitudinal studies and breeding programs.

Methodology:

R-based pipeline that applies QC metrics with user-defined filtering thresholds, generates QC reports, produces filtered datasets including a genomic relationship matrix, and constructs a database storing genotypic, phenotypic, and quality metrics for integration of new samples.