Crosshap: R package for local haplotype visualization for trait association analysis.

ABSTRACT:

Summary

Genome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, crosshap is equipped with visualization tools for choosing optimal clustering parameters (ɛ) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype com

SUBMITTER: Marsh JI 

PROVIDER: S-EPMC10471896 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature