LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files

• Published in: Briefings in bioinformatics Vol. 22; no. 4
• Main Authors: Dong, Shan-Shan, He, Wei-Ming, Ji, Jing-Jing, Zhang, Chi, Guo, Yan, Yang, Tie-Lin
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.07.2021; Oxford Publishing Limited (England)
• Subjects: Annotations; Format; Haplotypes; Linkage disequilibrium; Population genetics; Population studies; Single-nucleotide polymorphism; Subgroups; visualization; VCF files; haplotype block; linkage disequilibrium
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbaa227

Abstract The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03–13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.