ArchiLD: hierarchical visualization of linkage disequilibrium in human populations.

ABSTRACT: Linkage disequilibrium (LD) is an essential metric for selecting single-nucleotide polymorphisms (SNPs) to use in genetic studies and identifying causal variants from significant tag SNPs. The explosion in the number of polymorphisms that can now be genotyped by commercial arrays makes the interpretation of triangular correlation plots, commonly used for visualizing LD, extremely difficult in particular when large genomics regions need to be considered or when SNPs in perfect LD are not adjacent but scattered across a genomic region. We developed ArchiLD, a user-friendly graphical application for the hierarchical visualization of LD in human populations. The software provides a powerful framework for analyzing LD patterns with a particular focus on blocks of SNPs in perfect linkage as defi

SUBMITTER: Melchiotti R 

PROVIDER: S-EPMC3897757 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature