IMPUTE protocols

IMPUTE computational protocol

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


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Publications for IMPUTE

IMPUTE IN pipelines

PMCID: 5883389
PMID: 29682616
DOI: 10.21956/wellcomeopenres.15113.r31105

[…] standard of technical accuracy and robustness, and i have no suggestions for its improvement. one suggestion i offer the authors for their consideration is the possibility of using local snps to impute ccl3l1 cn from biobank data. clearly, any imputation of a multiallelic cnv from diallelic snps is likely to have limited power, but even incomplete imputation of ccl3l1 cn from snp data alone […]

PMCID: 5943470
PMID: 29608257
DOI: 10.1002/cam4.1445

[…] iselect array by the collaborative oncological gene‐environment study (“icogs”) 33, 34. snps not included on the icogs array were imputed (including all snps within 1 mb of the target snp) using impute(v2) software 35 and the 1000 genomes project (2012 release) as the reference panel 9. imputation quality scores ranged from 0.34 to 1.00. association testing on the icogs snps was performed […]

PMCID: 5341019
PMID: 28272483
DOI: 10.1038/srep43939

[…] using genome wide human snp array 6.0 (affymetrix, santa clara, ca, usa), which has been detailed previously31. for snps which were not genotyped in the arrays, we imputed the genotypes with the impute32 to facilitate the comparison of association results. the 1000 genome dataset was used as the reference data., bmi was adjusted for age and sex in a linear regression model. the resulting […]

PMCID: 5341021
PMID: 28272517
DOI: 10.1038/srep44114

[…] 17. association analysis was performed for males-only, females-only and combined male and female samples of hypertensive patients versus normotensive controls using snptest, the companion program to impute23536. a logistic regression model with additive genotype coding and with pc1, pc2, age, body mass index (bmi), and genotyping batch and genotyping array (5.0 vs. 6.0) as covariates was used […]

PMCID: 5404774
PMID: 28441463
DOI: 10.1371/journal.pone.0175957

[…] with the most frequent genotype based on the distribution of the snps genotypes (1, 2, or 3) across cases. for large numbers of missing genotypes, several established methods and tools, such as impute [60,61], beagle [62] and plink could be used., the pipeline is solely generic in use for the identification of key significant snps within candidate genes associated with continuous phenotypic […]

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

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