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IMPUTE specifications


Unique identifier OMICS_00062
Alternative name IMPUTE2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.3.2
Stability Stable
Maintained Yes


No version available

Publications for IMPUTE

IMPUTE citations


Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder

Sci Rep
PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y
call_split See protocol

[…] an additive model in linear regression in PLINK with age, IQ, sex and eigenvector 1 of PCA as covariates. Two-sided P < 5 × 10−8 was considered as genome-wide significance. We used MACH-admix 1.0 to impute non-genotyped SNPs using the ASN data (286 individuals) from the 1000 Genomes Project Integrated Phase 1 Release as the reference panel. Imputed SNPs with squared correlation between imputed an […]


Polygenic pleiotropy and potential causal relationships between educational attainment, neurobiological profile, and positive psychotic symptoms

PMCID: 5954124
PMID: 29765027
DOI: 10.1038/s41398-018-0144-4
call_split See protocol

[…] 907 autosomal SNPs.We then performed genotype imputation, using the phased haplotypes from the 1000 Genomes Project dataset as the reference panel. Prephasing and imputation was done with SHAPEIT and IMPUTE2,. The imputation was performed with the default parameters of the software. The final imputed dataset consisted of 9.7 million autosomal SNPs. […]


Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] 2 individuals of European ancestry to calculate linkage disequilibrium (LD) patterns. We used the software GTOOL-v0.7.5 ( to convert BMES IMPUTE2 data (both SNPs and Indels) to the plink format. This conversion changes A/T/G/C/I/D/R based allele coding to 1 or 2 (first and second allele). We extracted variant IDs, hg19 genomic locations […]


Global genetic differentiation of complex traits shaped by natural selection in humans

Nat Commun
PMCID: 5951811
PMID: 29760457
DOI: 10.1038/s41467-018-04191-y
call_split See protocol

[…] a were cleaned according to the following QC criteria: sample/SNP call rate <98%, MAF<0.01, and HWE test P<10-6. After QC, the SNP genotypes were imputed to the 1000G (phase 1) reference panels using IMPUTE2 (Supplementary Table ). The imputed SNPs with imputation INFO scores <0.3, MAF<0.01, or HWE P<10-6 in any of the populations (AFR, EAS, and EUR) were removed (Supplementary Table ), resulting […]


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

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

[…] in order to remove poorly 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 bi […]


Sex specific glioma genome wide association study identifies new risk locus at 3p21.31 in females, and finds sex differences in risk at 8q24.21

Sci Rep
PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z
call_split See protocol

[…] inberg equilibrium (HWE) (p < 1 × 10−5). Additional details of quality control procedures have been previously described in Melin et al.. All datasets were imputed separately using SHAPEIT v2.837 and IMPUTE v2.3.2 using a merged reference panel consisting of data from phase three of the 1,000 genomes project and the UK10K–.TCGA cases were genotyped on the Affymetrix Genomewide 6.0 array using DNA […]


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IMPUTE institution(s)
Department of Statistics, University of Oxford, Oxford, UK

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