Journal
BRIEFINGS IN BIOINFORMATICS
Volume 22, Issue 4, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbaa227
Keywords
linkage disequilibrium; haplotype block; visualization; VCF files
Funding
- National Natural Science Foundation of China [31871264, 31970569]
- Natural Science Foundation of Zhejiang Province [LWY20H060001]
- Fundamental Research Funds for the Central Universities
Ask authors/readers for more resources
LDBlockShow is an open source software that visualizes LD and haplotype blocks, providing faster speed and lower memory consumption compared to other tools.
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available