| Title: | LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files |
| Journal: | Briefings in Bioinformatics |
| Published: | 30 Oct 2020 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/33126247/ |
| DOI: | https://doi.org/10.1093/bib/bbaa227 |
| URL: | https://www.biorxiv.org/content/biorxiv/early/2020/06/15/2020.06.14.151332.full.pdf |
| Citations: | 239 (156 in last 2 years) as of 8 Aug 2024 |
Publication 9270
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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.</p>
6 Authors
- Shan-Shan Dong
- Wei-Ming He
- Jing-Jing Ji
- Chi Zhang
- Yan Guo
- Tie-Lin Yang
1 Application
| Application ID | Title |
|---|---|
| 46387 | Integration of regulatory elements and multi-trait genomic and phenomic data to improve the accuracy of risk prediction of human complex diseases/traits |
Enabling scientific discoveries that improve human health