PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

Chi Zhang; Shan-Shan Dong; Jun-Yang Xu; Wei-Ming He; Tie-Lin Yang

doi:10.1093/bioinformatics/bty875

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

Bioinformatics. 2019 May 15;35(10):1786-1788. doi: 10.1093/bioinformatics/bty875.

Authors

Chi Zhang^{1

2}, Shan-Shan Dong¹, Jun-Yang Xu², Wei-Ming He^{1

2}, Tie-Lin Yang¹

Affiliations

¹ Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.
² BGI Genomics, BGI-Shenzhen, Shenzhen, China.

PMID: 30321304
DOI: 10.1093/bioinformatics/bty875

Abstract

Motivation: Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay analysis from variant call format (VCF) files directly. In addition, generation of pair-wise LD measurements for whole genome SNPs usually resulting in large storage wasting files.

Results: We developed PopLDdecay, an open source software, for LD decay analysis from VCF files. It is fast and is able to handle large number of variants from sequencing data. It is also storage saving by avoiding exporting pair-wise results of LD measurements. Subgroup analyses are also supported.

Availability and implementation: PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genetic Linkage
Genetic Variation*
Linkage Disequilibrium
Polymorphism, Single Nucleotide
Software*