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Protocols

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 citations

 (231)
library_books

Genome wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

2018
Nat Commun
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 wa […]

library_books

Genetic susceptibility markers for a breast colorectal cancer phenotype: Exploratory results from genome wide association studies

2018
PLoS One
PMCID: 5919670
PMID: 29698419
DOI: 10.1371/journal.pone.0196245

[…] The imputation of un-typed SNPs was performed on the merged dataset from 1000 Genomes CEPH data reference panels (Phase 1 Version 3, NCBI build 37 [hg19]) using MaCH 1.0.16 [] and MiniMac (2012-05-29 release) from 1000 genomes Phase I V3 20101123 release EUR reference panel of 1092 samples []. SNPs with quality scores of <0.8 were removed. After imputation, filtering on minor a […]

library_books

Stage 1 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis

2018
Wellcome Open Res
PMCID: 5904730
PMID: 29744390
DOI: 10.21956/wellcomeopenres.15031.r30762

[…] s phased and imputed genotypes using high-density reference panels. Variant Call Files (VCF) were uploaded for 15,936 SNPs genotyped on chromosome 7. Genotypes were phased within Eagle and imputed by Minimac against the Human Reference Panel hrc.r1.1.2016, which includes 64,940 haplotypes of predominantly European ancestry. In total, genotypes were generated for 2,289,829 SNPs across chromosome 7, […]

call_split

A Common Allele in FGF21 Associated with Sugar Intake Is Associated with Body Shape, Lower Total Body Fat Percentage, and Higher Blood Pressure

2018
Cell Rep
PMCID: 5912948
PMID: 29641994
DOI: 10.1016/j.celrep.2018.03.070
call_split See protocol

[…] , 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 mode […]

library_books

Pleiotropic Contribution of MECOM and AVPR1A to Aggression and Subcortical Brain Volumes

2018
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 using an i […]

library_books

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

2018
PMCID: 5861640
PMID: 29581880
DOI: 10.1186/s40104-018-0241-5

[…] populations [], the size of the reference population [, ], sequencing depth [], and SNP density of the target panel []. With a layer chicken population, Ni et al. [] evaluated performance of FImpute, Minimac and IMPUTE2 by imputing Affymetrix® Axiom® high-density SNP (600 K) data to WGS data, and FImpute was reported to be slightly worse than Minimac and IMPUTE2 in terms of genotype correlation. P […]

Citations

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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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