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

被引：313

作者：

Dong, Shan-Shan ^{[1
]}

He, Wei-Ming ^{[2
]}

Ji, Jing-Jing ^{[2
]}

Zhang, Chi ^{[2
]}

Guo, Yan ^{[1
]}

Yang, Tie-Lin ^{[1
]}

机构：

[1] Xi An Jiao Tong Univ, Sch Life Sci & Technol, Key Lab Biomed Informat Engn, Minist Educ, Xian 710049, Peoples R China

[2] BGI Genom, Shenzhen, Peoples R China

来源：

BRIEFINGS IN BIOINFORMATICS | 2021年 / 22卷 / 04期

基金：

中国国家自然科学基金;

关键词：

linkage disequilibrium; haplotype block; visualization; VCF files;

D O I：

10.1093/bib/bbaa227

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

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