Linkage disequilibrium refers to the association of genes in a population. Linkage, on the other hand, tells us whether genes are on the same chromosome in an individual. There is no necessary relationship between the two. Genes that are closely linked may or may not be associated in populations.

Calculating LD decay. One of the most common questions we get before running a genome scan analysis is - what size should my sliding window be? There is really no correct way to answer this as it the answer is dependent on your aims and the purpose/scale of the genome scan.

Linkage disequilibrium (LD) mapping of a disease-associated allele is based on the slow decay of LD with closely linked markers.

Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the …

Oct 15, 2018 · 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.

Nov 14, 2019 · This tutorial introduces the concept of linkage disequilibrium (LD) using sample data. LD and LD decay in a gene are estimated using GGT2 software.

Linkage disequilibrium (LD) analysis is fundamental to the investigation of the genetic architecture of complex traits (e.g. human disease, animal and plant breeding) and population structure and evolution dynamics.

Here, we introduce PopLDdecay, a simple- efficient software for LD decay analysis, which processes the Variant Call Format (VCF)[5] file to produce the LD decay statistics results and plot the LD decay graphs.

Feb 12, 2022 · LD衰减（LD decay）： 指位点之间由连锁不平衡到连锁平衡的演变过程，能够很好的反映连锁不平衡程度。 PopLDdecay是一款基于VCF文件，快速、高效计算连锁不平衡的工具。 相比于 PLINK 和 Haploview，PopLDdecay 的优点如下： 支持 subgroup 的分析。 运行. 2. 计算LD decay. 输出文件中为LD衰减的计算结果，包括平均R2，平均D'等。 准备亚群的名称清 …

May 15, 2019 · 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.