GHap

GHap calls haplotypes from phased marker data and scores sample HapGenotype by HapAllele dosage (0, 1, or 2) within user-defined HapBlock regions to support multi-allelic haplotype analyses.

Key Features:

• HapBlock: Uses user-defined haplotype blocks (HapBlock) to delineate haplotype regions.
• HapAllele identification: Identifies and characterizes distinct haplotype alleles (HapAllele) present in the dataset.
• HapGenotype scoring: Scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dosage values 0, 1, or 2.
• Multi-allelic marker support: Handles multi-allelic markers in addition to analyses applicable to bi-allelic markers.
• Output compatibility: Produces output formatted for integration with data processing pipelines designed for bi-allelic markers.
• Input data: Operates on phased marker data as input.

Scientific Applications:

• Association studies: Haplotype-based association analyses that leverage multi-allelic information.
• Population genetics: Analyses of haplotype diversity and population structure using haplotype allele information.
• Evolutionary biology: Studies of haplotype evolution and allele frequency dynamics across HapBlock regions.

Methodology:

Accepts phased marker data and uses predefined HapBlock configurations to identify HapAlleles and score HapGenotypes by HapAllele dosage (0, 1, 2).