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Minimac2 specifications

Information


Unique identifier OMICS_31632
Name Minimac2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
gcc, OpenBlas, GFortran
Source code URL http://csg.sph.umich.edu/cfuchsb/minimac2.2014.9.15.src.tgz
Maintained Yes

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Maintainer


  • person_outline Christian Fuchsberger

Publication for Minimac2

Minimac2 citations

 (27)
library_books

Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

2018
BMC Genet
PMCID: 5948690
PMID: 29751743
DOI: 10.1186/s12863-018-0620-0

[…] orly imputed markers that might have adverse effects on the imputation procedures.Imputation from 54 k to HD genotypes to HD and imputation to the WGS level were undertaken with IMPUTE2 v2.3.1 [] and Minimac2 [], respectively. The imputation to whole genome sequence was done in chunks of 5 Mb with the length of buffer region of 0.25 Mb on either side. A total of 22,751,039 biallelic variants were […]

library_books

Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey

2018
PLoS Genet
PMCID: 5886383
PMID: 29621232
DOI: 10.1371/journal.pgen.1007275

[…] We also imputed the X chromosome using with the 1000 Genomes Project Phase 3 v5 reference panel. We imputed male (n = 3,927) and female (n = 4,476) samples separately, using Mach for pre-phasing and Minimac2 for imputation. Imputation yielded data for 47,095,001 variants, and the 534,143 directly genotyped variants were also assigned imputed genotypes. We removed variants with an imputation r2 <0 […]

library_books

Genome wide analyses of self reported empathy: correlations with autism, schizophrenia, and anorexia nervosa

2018
PMCID: 5845860
PMID: 29527006
DOI: 10.1038/s41398-017-0082-6

[…] ompared to the reference European 1000 Genomes data (χ2 P < 10−15). We then imputed each phased segment against all-ethnicity 1000 Genomes haplotypes (excluding monomorphic and singleton sites) using Minimac2, using 5 rounds and 200 states for parameter estimation. We restricted the analyses to only SNPs that had a minor allele frequency of at least 1%. For genotyped SNPs, those present only on pl […]

call_split

Exposure to Night Time Traffic Noise, Melatonin Regulating Gene Variants and Change in Glycemia in Adults

2017
PMCID: 5750910
PMID: 29194408
DOI: 10.3390/ijerph14121492
call_split See protocol

[…] e frequency (MAF) of <5% or deviation from Hardy–Weinberg equilibrium (HWE) at a threshold of 10−6 were also excluded. G1 and G2 datasets were phased using ShapeIT version 2.r790 [] and imputed using MiniMac2 []. The imputed datasets were then merged, after excluding variants with low imputation quality (R2 < 0.3), yielding ~14 million markers for 4324 participants across G1 and G2, from where we […]

library_books

Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment

2017
Am J Hum Genet
PMCID: 5812923
PMID: 29198719
DOI: 10.1016/j.ajhg.2017.10.001

[…] l/HaploReg, http://archive.broadinstitute.org/mammals/haploreg/IMPUTE2, http://mathgen.stats.ox.ac.uk/impute/impute_v2.htmlIntegrative Genomics Viewer, http://software.broadinstitute.org/software/igv/Minimac2, https://genome.sph.umich.edu/wiki/Minimac2Mouse Genome Informatics, http://www.informatics.jax.org/OMIM, http://www.omim.org/PubMed, https://www.ncbi.nlm.nih.gov/pubmed/SHAPEIT, http://mathg […]

call_split

Genetic Variants Associated With Uncontrolled Blood Pressure on Thiazide Diuretic/β‐Blocker Combination Therapy in the PEAR (Pharmacogenomic Evaluation of Antihypertensive Responses) and INVEST (International Verapamil‐SR Trandolapril Study) Trials

2017
PMCID: 5721751
PMID: 29097388
DOI: 10.1161/JAHA.117.006522
call_split See protocol

[…] notypes of variants that passed quality control underwent haplotype phasing in Markov Chain Haplotyping (MaCH) software followed by imputation to 1000 Genomes phase III reference panels using minimac/minimac2., Variants with imputation quality r 2<0.30 and minor allele frequency <3% were excluded.INVEST DNA samples were genotyped on the Illumina OmniExpressExome Beadchip (Illumina, San Diego, CA) […]

Citations

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Minimac2 institution(s)
Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA; 23andMe, Inc., Mountain View, CA, USA
Minimac2 funding source(s)
Supported by National Institutes of Health research grants.

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