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

By Shanshan Dong, Wei-Ming He, Jing-Jing Ji, Chi Zhang, Yan Guo, Tie-Lin Yang. bioRxiv, 2020

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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, and direct calculation from variant call format (VCF) files is not supported. Here we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from VCF files. It is time and memory saving. In a test dataset with 100 SNPs from 60,000 subjects, it was at least 429.03 times faster and used only 0.04% – 20.00% of physical memory as compared to 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 large number of SNPs and support subgroup analysis. This fast and convenient tool would facilitate the visualization of LD and haplotype blocks for geneticists.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b926f29ffb30b8e51615e92cdcf36a8fa532f8a1