BAFRegress

BAFRegress detects and estimates within-species DNA sample contamination from B allele frequency (BAF) data derived from Illumina genotyping arrays using a regression model.

Key Features:

• Contamination detection and estimation: Identifies within-species DNA sample contamination and estimates contamination levels as low as 1%.
• Regression model utilization: Applies a regression model to B allele frequency (BAF) data to produce quantitative contamination estimates.
• Supported input data: Analyzes BAF from Illumina genotyping arrays and supports analysis of sequencing reads and array-based genotype data.
• Pre-sequencing screening: Enables detection of contamination using array-based genotype data prior to sequencing to protect genotype accuracy.

Scientific Applications:

• Genotype quality control: Detects contamination that can cause systematic genotype misclassification and false positive associations in genetic studies.
• Pre-sequencing sample screening: Screens samples with array-based BAF data before sequencing to identify contaminated samples and reduce downstream sequencing costs.

Methodology:

Analyzes B allele frequency (BAF) data derived from Illumina genotyping arrays and applies a regression model to estimate contamination; it can also analyze sequencing reads and array-based genotype data to detect contamination prior to sequencing.