ImpG-Summary – Imputation from summary statistics

Impution using external reference panels(e.g. 1000Genomes) is a widely used approach for increasing power in GWAS and meta-analysis. We developed software for Gaussian imputation from summary association statistics; it takes as input 1000 Genomes reference haplotypes and summary association statistics at a typed set of SNPs from a GWAS or meta-analysis. It outputs summary association statistics at all 1000 Genomes variants.

ImpG-Summary is described here:
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.
Pasaniuc B, Zaitlen N, Shi H, Bhatia G, Gusev A, Pickrell J, Hirschhorn J, Strachan DP, Patterson N, Price AL. Bioinformatics 2014.

Stable release (v1.0 July 2013) can be downloaded here. The latest working version of the code can be downloaded from github here. The pdf manual is located here.

Imputed Z-scores using ImpG-Summary to 1000 Genomes reference panels starting from Teslovich et al meta-analysis of lipids traits can be downloaded here (HDL, LDL, TC, TG). The column ID can be found here. Only Z-scores imputed at an r2pred > 0.6 are present in the files. For all imputed data please contact Bogdan.

Please contact Huwenbo (shihuwenbo_AT_ucla.edu) or Bogdan (bpasaniuc_AT_mednet.ucla.edu) for any comments or suggestions related to the software.

The software is free for non-commercial use, and may be licensed for commercial use.

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This web-site is based upon work supported by the National Institutes of Health under awards R01 HG006399, R03 CA162200 and R01 GM053275. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies above.