Michigan Imputation Server statistics

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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)
2017
PMCID: 5453576
PMID: 28570605
DOI: 10.1371/journal.pone.0178700

[…] gse90878. genomic dna extraction, genotyping on the illumina humanomniexpress-12 v1.1 beadchip array, and quality-control were performed as previously described []. genotypes were imputed using the michigan imputation server with the haplotype reference consortium (hrc) panel (v. r1.1)[]., allelic imbalance (ai) was measured at each heterozygous genotype covered by rna-sequencing in the 24 […]

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

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


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Michigan Imputation Server in publications

 (32)
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z

[…] datasets have been excluded. ancestry outliers were identified in tcga using principal components analysis in plink 1.9. resulting files were imputed using eagle 2 and minimac3 as implemented on the michigan imputation server (https://imputationserver.sph.umich.edu) using the haplotype reference consortium version r1.1 2016 as a reference panel–. somatic characterization of tcga cases […]

PMCID: 5940825
PMID: 29739930
DOI: 10.1038/s41467-018-03621-1

[…] was used to perform some final filtering and split data by chromosome. phasing (via eagle v2.3) and imputation against the hrc r1.1 2016 panel (via minimac3) were carried out by the michigan imputation server., european samples had been split into ten groups during imputation to ease the computational burden on the michigan server, so after obtaining the imputed .vcf files, […]

PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] as reference panels. specifically, snp genotypes were imputed in two steps. first, genotypes on each chromosome were phased using shapeit (v2.r837). then, phased data were submitted to the michigan imputation server, and imputed using minimac3. the protocol of the study was approved by the institutional review board of brigham and women’s hospital and the harvard school of public […]

PMCID: 5895806
PMID: 29643358
DOI: 10.1038/s41398-018-0124-8

[…] samples with european ancestry were retained by visual inspection (overlapping with ceu and tsi, figure ). following these steps 4733 samples and 204,597 markers were retained for imputation. the michigan imputation server was used for genetic imputation of the pnc data (minimac3 for imputation and hapi-ur for phasing) with the 1000 genome phase 3 data as reference panel resulting in a total […]

PMCID: 5892035
PMID: 29631575
DOI: 10.1186/s12931-018-0762-7

[…] snps. an additional 133 samples were removed because they failed subsequent quality control, which resulted in a final sample of n = 4048 for the present analysis. imputation was undertaken with the michigan imputation server [] using the haplotype reference consortium (hrc) [] panel. variants were excluded if the imputation r2 was < 0.5 and if the minor allele frequency was < 1%., […]


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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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