LinkImpute specifications

Information

Unique identifier	OMICS_19552
Name	LinkImpute
Alternative name	LinkImputeR
Software type	Application/Script
Interface	Command line interface
Restrictions to use	None
Input data	Some next-generation DNA sequence data.
Input format	VCF
Operating system	Unix/Linux
Computer skills	Advanced
Stability	Stable
Source code URL	http://www.cultivatingdiversity.org/uploads/5/8/2/9/58294859/linkimputer-src.tar.gz
Maintained	Yes

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Maintainer

Daniel Money <>

Publications for LinkImpute

LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

2017 BMC Genomics

PMCID: 5504746

PMID: 28693460

DOI: 10.1186/s12864-017-3873-5

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.

2015 G3

PMCID: 4632058

PMID: 26377960

DOI: 10.1534/g3.115.021667

LinkImpute IN pipelines

(2)

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

2017

PMCID: 5716196

PMID: 29036322

DOI: 10.1093/nar/gkx853

[…] snp calling methods., genetic maps were constructed from 70% mcr, 50% mcr and 20% mcr tgbs (grl2) snp sets in the ibm rils with the same filtering described for segmentation using asmap (32). linkimpute (33) was run with the default settings. snps imputed from linkimpute and unimputed snps for each mcr were imported into asmap (32) for map construction. rils with high similarity […]

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

2017

PMCID: 5716196

PMID: 29036322

DOI: 10.1093/nar/gkx853

[…] 50% mcr and 20% mcr tgbs (grl2) snp sets in the ibm rils with the same filtering described for segmentation using asmap (32). linkimpute (33) was run with the default settings. snps imputed from linkimpute and unimputed snps for each mcr were imported into asmap (32) for map construction. rils with high similarity were detected using the comparegeno function. six rils (m0122, m0173, m0177, […]

LinkImpute institution(s)

Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada

LinkImpute funding source(s)

Supported by a Genome Canada Bioinformatics and Computational Biology grant; the Canada Research Chairs program; and the National Sciences and Engineering Research Council of Canada.

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