haploview

Haploview is a software package used for analyzing genetic association data. It was developed by the Broad Institute and is freely available for academic and non-profit use. The primary function of Haploview is to visualize and analyze haplotype blocks, identify tag SNPs, and perform basic association tests.

The software reads standard genetic association data formats, such as PLINK and VCF. It then allows users to visually inspect linkage disequilibrium (LD) patterns within specified genomic regions. LD is a measure of the non-random association of alleles at different loci. Haploview uses pairwise r-squared values or D' to represent LD, often displayed as a heat map.

A key feature of Haploview is its ability to identify tag SNPs. Tag SNPs are a subset of SNPs that capture most of the genetic information in a region, reducing the number of SNPs that need to be genotyped in association studies. Various algorithms are available within Haploview to select these tag SNPs.

Furthermore, Haploview can perform simple association tests, such as chi-squared tests and Fisher's exact tests, to assess the relationship between genotypes or haplotypes and a phenotype. It also supports the import and visualization of population structure information, such as principal component analysis results. The graphical interface makes it accessible for researchers to explore complex genetic data without extensive programming knowledge.