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Protocols

PopLDdecay specifications

Information


Unique identifier OMICS_32536
Name PopLDdecay
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux
Programming languages C, C++, Perl, Shell (Bash)
License MIT License
Computer skills Advanced
Version 3.40
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Tie-Lin Yang
  • person_outline Wei-Ming He

Publication for PopLDdecay

PopLDdecay citations

 (4)
library_books

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

2017
Nat Commun
PMCID: 5741661
PMID: 29273740
DOI: 10.1038/s41467-017-02445-9

[…] most likely number of sub-populations and to graphically represent the sub-population membership of each accession.LD (r 2) was calculated for all pairs of SNPs after imputation within 5000 kb using PopLDdecay software (version 1.01, https://github.com/BGI-shenzhen/PopLDdecay). The following parameters were used: -MaxDist 5000 -MAF 0.05 -Het 0.88 -Miss 0.25. The maximum value of r 2 was calculate […]

call_split

The genetic architecture of amylose biosynthesis in maize kernel

2017
Plant Biotechnol J
PMCID: 5787843
PMID: 28796926
DOI: 10.1111/pbi.12821
call_split See protocol

[…] o retain only MAF >0.05 were generated by Dr. Lai's laboratory at China Agricultural University (Liu et al., ). The decay distance of linkage disequilibrium in the association panel was calculated by PopLDdecay (https://github.com/BGI-shenzhen/PopLDdecay) with all SNP markers and mixed linear model (MLM) GWAS was carried out using the EMMAX suite (Kang et al., ). EMMAX‐kin was used to calculate th […]

library_books

Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association Mapping Panel Revealed by Genome Wide SNP Markers in Sesame

2017
Front Plant Sci
PMCID: 5498554
PMID: 28729877
DOI: 10.3389/fpls.2017.01189

[…] opulation structure) by pairwise comparisons among the 44,109 SNP markers [missing rates <0.30 and minor allele frequency (MAF) ≥0.05] using r2. For all pairs of SNPs, the r2 was calculated using the PopLDdecay v.3.26 program. […]

library_books

Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome wide SNPs Developed by Genotyping by sequencing and SSR Markers

2017
Front Plant Sci
PMCID: 5394126
PMID: 28458680
DOI: 10.3389/fpls.2017.00575

[…] D between 4,680 genome-wide SNPs for all pseudo-chromosomes and individual pseudo-chromosomes in 150 Chinese jujube accessions was calculated based on the allele frequency correlations (r2) using the PopLDdecay program. The LD decay was calculated when the r2 value decreased below a threshold level (i.e., r2 < 0.1). Mean r2 values were used to calculate the LD using a 100-kb sliding window-based a […]


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PopLDdecay institution(s)
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; BGI Genomics, BGI-Shenzhen, Shenzhen, China
PopLDdecay funding source(s)
Supported by the National Natural Science Foundation of China (31701095 and 81573241); China Postdoctoral Science Foundation (2016M602797, 2018T111038); Natural Science Basic Research Program Shaanxi Province (2018JQ3058); Innovative Talent Promotion Plan of Shaanxi Province for Young Sci-Tech New Star (2018KJXX-010) and the Fundamental Research Funds for the Central Universities.

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