minimac protocols

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minimac specifications

Information


Unique identifier OMICS_08953
Name minimac
Alternative name Minimac3
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data M3VCF files
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
cget, cmake
Maintained Yes

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Publication for minimac

minimac in pipelines

 (6)
2017
PMCID: 5520280
PMID: 28174340
DOI: 10.1136/thoraxjnl-2016-208448

[…] using the 1000 genomes project reference panel (1000g phase i integrated release v.3 (march 2012)). chunking was performed using chunkchromosome, phasing using mach (v.1.0.18) and imputation using minimac (v.2012.10.3). variants where imputation quality (r2) was <0.3 or maf <1% were excluded., data on age and smoking were checked for consistency over time. where possible, missing data […]

2016
PMCID: 4900668
PMID: 27280446
DOI: 10.1371/journal.pone.0156914

[…] against previous genotype data, where available. no maf cut-off was applied at this stage. imputation was done on cleaned genotypes in three phases—chunking, phasing and imputing—using the mach1 and minimac software [, ] and applying the strategy described at minimac:1000 genomes imputation cookbook. the resulting file contained ~4.5 million autosomal snps (r2 > 0.3, maf > 0.001). the data […]

2015
PMCID: 4564946
PMID: 26014426
DOI: 10.1038/ejhg.2015.102

[…] 1094 individuals and 2188 haplotypes and the program mach 1.0.16. the variants in the build-37 november 2010 release of 1000 genomes (phase 1-α interim) were imputed into the phased haplotypes using minimac. this resulted in 37 426 733 imputed snps. we excluded snps that were imputed with an r2imp<0.5. this left 10 879 115 snps and after filtering for minor allele frequency (maf)>0.01 […]

2015
PMCID: 4584317
PMID: 26184321
DOI: 10.3390/genes6030559

[…] maf was between 0.35 and 0.50 to avoid incorrect strand alignment., phasing of all samples and imputing cross-missing platform snps was done with mach 1 [,]. the phased data were then imputed with minimac [] in batches of around 500 individuals for 561 chromosome chunks obtained by the chunkchromosome program []. after imputation, dna confirmed mz twins were re-duplicated back into the data. […]

2015
PMCID: 4848212
PMID: 26503814
DOI: 10.1038/tpj.2015.65

[…] based on cluster plots (genotyped) and imputation quality (r2 ≥ 0.80) for imputed snps, hardy-weinberg equilibrium (p-value), and missingness (% threshold). imputation was performed using mach and minimac with 1000 genomes phase i v 3 european reference panels for white subjects. cosmopolitan reference panels were used for copdgene aa subjects. variants with a minor allele frequency (maf) < […]


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minimac in publications

 (220)
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] the 1000 genomes project. after quality control, 532,488 autosomal variants were phased using eagle2 and subsequently imputed up to the reference panel from the 1000 genomes project phase 3 using minimac3., variants with good imputation quality (minimac rsq >0.3) were tested for associations with two quantitative traits, age at menarche and age at menopause, and two dichotomous traits, […]

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

[…] the ommoord municipality of rotterdam, the netherlands. subjects were genotyped using the infinium ii humanhap550 k and human 610 quad arrays of illumina. imputation was performed using the mach and minimac software packages and the 1000 genomes project (phase 1, integrated variant set across 1092 individuals, v2, march 2012) as the reference panel, as described elsewhere. ease of skin tanning […]

PMCID: 5910407
PMID: 29679049
DOI: 10.1038/s41598-018-24774-5

[…] maternal age at first childbirth was encoded in years. higher composite scores reflect higher ses., genome-wide genotyping data was obtained in two waves of genotyping, and imputed using minimac3 to the haplotype reference consortium reference data (supplementary material,–). details on quality control and imputation are included in the supplementary methods. following qc, genotyped […]

PMCID: 5912948
PMID: 29641994
DOI: 10.1016/j.celrep.2018.03.070

[…] genotyping, and gene expression and eqtl analyses have been described previously for each of the three studies (, , ) genotypes were imputed to the 1000 genomes project phase 1 reference panel with minimac (https://genome.sph.umich.edu/wiki/minimac), and expression probe sequences were mapped to ensembl genes. within each dataset, a genome-wide eqtl analysis was run with an additive genetic […]

PMCID: 5891600
PMID: 29666571
DOI: 10.3389/fnbeh.2018.00061

[…] identify specific genetic contributions to individual volumes. genomic data comprised only european samples and were imputed to the 1000 genomes, v3 phase1 reference panel using mach for phasing and minimac for imputation (fuchsberger et al., ). gwas was performed at each site, and snps with an imputation score of rsq < 0.5 and minor allele count <10 were removed. results were combined […]


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minimac 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, 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
minimac funding source(s)
Supported by National Institutes of Health grants HG007022, HL117626, HG000376, R01DA037904, Austrian Science Fund grant J-3401, the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement 602133, and the Intramural Research Program of the National Institute on Aging, National Institutes of Health.

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