SHAPEIT

SHAPEIT estimates haplotypes and performs phasing and imputation from genotype and sequencing data to infer diploid phase information for studies of human-disease etiology and large-scale genomic analyses.

Key Features:

• Improved accuracy and speed: Enhances accuracy and computational speed compared to several existing widely-used methods.
• Scalability: Scales linearly with the number of haplotypes used in each iteration, enabling efficient processing of whole chromosomes.
• Versatility: Applicable to genotype data from unrelated samples or small nuclear families.
• Segmented approach: Implements a segmented haplotype estimation and imputation strategy to manage large genomic datasets.

Scientific Applications:

• Human-disease etiology: Provides detailed phase information about diploid sequences to aid elucidation of genetic contributions to disease.
• Genomic studies: Supports comprehensive genomic analyses, including whole-chromosome phasing and imputation for large datasets.

Methodology:

SHAPEIT employs a segmented approach to haplotype estimation and imputation and leverages linear scaling with the number of haplotypes used in each iteration to enable efficient computation across extensive genomic datasets.