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IMPUTE specifications

Information


Unique identifier OMICS_00062
Name IMPUTE
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

 (73)
2018
PMCID: 5805680
PMID: 29422604
DOI: 10.1038/s41467-018-02942-5

[…] omni1m arrays at the cgr of the division of cancer epidemiology and genetics, nci, nih. after quality control, genotypes were imputed using the 1000 g (phase 1, v3) imputation reference data set and impute 2. pre-imputation exclusion filters of hardy weinberg equilibrium p < 1 × 10−6, minor allele frequency (maf) <0.01, genotype missing rate >0.05, a/t and g/c pairs on ambiguous dna […]

2018
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 […]

2017
PMCID: 5226683
PMID: 28076348
DOI: 10.1371/journal.pgen.1006516

[…] haploview: https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview, impute2: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html, locuszoom: http://locuszoom.sph.umich.edu/locuszoom/, metasoft: http://genetics.cs.ucla.edu/meta, oragene discover kit ogr-250 by dna […]

2017
PMCID: 5316867
PMID: 28195176
DOI: 10.1038/ncomms14418

[…] analysis was performed as described in a previous publication. germline genotypes of these patients were genotyped on the illumina 2.5m exome v1.0 and imputed to 1000 genomes phase 3 release using impute2. for cis-eqtl analysis, we normalized gene quantification separately for healthy and tumour samples. technical covariates were discovered using the peer programme and 20 peer factors […]

2017
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 previously. for snps which were not genotyped in the arrays, we imputed the genotypes with the impute 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 […]


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IMPUTE in publications

 (889)
PMCID: 5954124
PMID: 29765027
DOI: 10.1038/s41398-018-0144-4

[…] 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., t-tests, chi-square tests, or multivariable […]

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

[…] individuals of european ancestry to calculate linkage disequilibrium (ld) patterns. we used the software gtool-v0.7.5 (http://www.well.ox.ac.uk/%7ecfreeman/software/gwas/gtool.html) 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 […]

PMCID: 5951811
PMID: 29760457
DOI: 10.1038/s41467-018-04191-y

[…] {upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$p < 10^{ - 6}$$\end{document}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 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepacka […]

PMCID: 5943590
PMID: 29743610
DOI: 10.1038/s41598-018-24580-z

[…] all cases and frequencies may not add to 100%., **differs between included studies at the p < 0.05 level., there were 5,934 snps within 500 kb of 26 previously discovered glioma risk loci with impute2 information score (info) > 0.7 and maf > 0.01 that were previously found to have at least a nominal (p < 5 × 10−4) association with glioma, and results were considered significant […]

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

[…] that was designed to study the genetics of lung health and disease. the uk10k haplotype reference and the 1000 genomes phase 3 reference panels were merged and used as reference panel in the impute2 software. kinship coefficients for all pairs were calculated using king’s robust estimator and used to identify and remove related individuals. imputation, relatedness assessment and quality […]


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

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