Michigan Imputation Server protocols

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description
Michigan Imputation Server computational protocol

Michigan Imputation Server specifications

Information


Unique identifier OMICS_17672
Name Michigan Imputation Server
Interface Web user interface
Restrictions to use None
Input format VCF files compressed by bgzip.
Computer skills Basic
Version 1.22.0
Stability Stable
Maintained Yes

Documentation


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Publication for Michigan Imputation Server

Michigan Imputation Server IN pipelines

 (2)
2018
PMCID: 5879874
PMID: 29619113
DOI: 10.1186/s12263-018-0597-3

[…] about this dataset can be found in carayol et al. [17]. briefly, 498,233 single nucleotide polymorphisms (snps) were genotyped; after quality check, additional snps were imputed using the michigan imputation server [18] and the european 1000 genomes set reference panel. snp information was mapped onto ncbi version 37. information was available for 4,020,654 snps in 494 participants […]

2017
PMCID: 5553663
PMID: 28800727
DOI: 10.1186/s12864-017-4013-y

[…] frequency (maf) < 0.01, that violated hardy-weinberg equilibrium (hwe), and had more than 0.05 missing genotype information [12]. genotypes for a total of 560,170 snps were imputed using the michigan imputation server [13], the 1000 genomes phase 3 v5 reference panel, and the eagle phasing algorithm to obtain phased output [14, 15]. we developed a python script based on vcf and pysam […]

Michigan Imputation Server institution(s)
Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA; Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy; Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA; Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, US National Institutes of Health, Bethesda, MD, USA; HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Psychology, University of Minnesota, Minneapolis, MN, USA; Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Neurobiology–Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, MD, USA; Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), affiliated with the University of Lübeck, Bolzano, Italy
Michigan Imputation Server funding source(s)
Supported by the National Institutes of Health grants HG007022 and HL117626, HG000376, and R01DA037904, Austrian Science Fund grant J-3401, the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement 602133 and also in part by the Intramural Research Program of the National Institute on Aging, National Institutes of Health.

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