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ImpG-Summary specifications

Information


Unique identifier OMICS_07885
Name ImpG-Summary
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data ImpG-Summary takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis.
Output data It outputs summary association statistics at all 1000 Genomes variants.
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bogdan Pasaniuc

Publication for ImpG-Summary

ImpG-Summary citations

 (3)
call_split

Discovery and fine mapping of adiposity loci using high density imputation of genome wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium

2017
PLoS Genet
PMCID: 5419579
PMID: 28430825
DOI: 10.1371/journal.pgen.1006719
call_split See protocol

[…] nel (Phase I Integrated Release Version 3) using the ImpG program []. In brief, palindromic variants (AT/CG) and variants with allele mismatch with the reference were removed from the data. Using the ImpG-Summary method, the z-score of an unobserved variant was calculated as a linear combination of observed z-scores weighted by the variance-covariance matrix between variants induced by LD within a […]

library_books

Identification of shared risk loci and pathways for bipolar disorder and schizophrenia

2017
PLoS One
PMCID: 5293228
PMID: 28166306
DOI: 10.1371/journal.pone.0171595

[…] Genomes Project, February 2012 release; and HapMap phase 2 CEU, respectively). Therefore, the summary statistics of the PGC BD GWAS [] were imputed using the 1,000 Genomes Project reference panel and ImpG-Summary. The latter is a recently proposed method for the rapid and accurate imputation of summary statistics []. This resulted in z-scores for >20 million SNPs. A total of 111 SCZ-associated SNP […]

library_books

Bias Characterization in Probabilistic Genotype Data and Improved Signal Detection with Multiple Imputation

2016
PLoS Genet
PMCID: 4910998
PMID: 27310603
DOI: 10.1371/journal.pgen.1006091

[…] he suitability of MI to a given application is restricted to situations where the probability-generating method is itself appropriately suited.Recent work ([–]) has produced algorithms (MIX, DISTMIX, ImpG-Summary) capable of imputing association statistics from summary data, without the need for individual-level genotype information. These methods offer substantial time savings relative to genotyp […]

Citations

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ImpG-Summary institution(s)
Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA

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