Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.

Abstract excerpt

We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype-calling methods,...

Topics

• Algorithms
• Alleles
• Data Interpretation, Statistical
• False Positive Reactions
• Genetic Markers
• Genome-Wide Association Study
• Genotype
• Haplotypes
• Humans
• Models, Statistical
• Oligonucleotide Array Sequence Analysis
• Probability
• Reproducibility of Results
• Software