PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
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 result...
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| Published in | Bioinformatics Vol. 35; no. 10; pp. 1786 - 1788 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
15.05.2019
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| Subjects | |
| Online Access | Get full text |
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| Abstract | 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. |
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| AbstractList | 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.
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.
PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay. 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.MOTIVATIONLinkage 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.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.RESULTSWe 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.PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay.AVAILABILITY AND IMPLEMENTATIONPopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay. 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. 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. 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. PopLDdecay is freely available at https://github.com/BGI-shenzhen/PopLDdecay. |
| Author | Xu, Jun-Yang Zhang, Chi Yang, Tie-Lin He, Wei-Ming Dong, Shan-Shan |
| Author_xml | – sequence: 1 givenname: Chi surname: Zhang fullname: Zhang, Chi organization: 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 – sequence: 2 givenname: Shan-Shan surname: Dong fullname: Dong, Shan-Shan organization: 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 – sequence: 3 givenname: Jun-Yang surname: Xu fullname: Xu, Jun-Yang organization: BGI Genomics, BGI-Shenzhen, Shenzhen, China – sequence: 4 givenname: Wei-Ming surname: He fullname: He, Wei-Ming email: hewm@genomics.cn organization: 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 – sequence: 5 givenname: Tie-Lin surname: Yang fullname: Yang, Tie-Lin email: yangtielin@mail.xjtu.edu.cn organization: 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 |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30321304$$D View this record in MEDLINE/PubMed |
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| Copyright | The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2018 The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. |
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| Snippet | Abstract
Motivation
Linkage disequilibrium (LD) decay is of great interest in population genetic studies. However, no tool is available now to do LD decay... 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... |
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| SubjectTerms | bioinformatics computer software genome linkage disequilibrium |
| Title | PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files |
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