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PEPIS (Pipeline for estimating EPIStatic genetic effects) is a web-based tool for the estimation of polygenic Epistatic QTL mapping for genome-wide association studies (GWAS). The PEPIS algorithm uses a new linear mixed model and includes kinship matrix calculation, polygenic component analyses, and genome scanning for main and epistatic effects.


Mapping; GWAS study; Genetics


  • Operation: Mapping
  • Software interface: Web user interface
  • Language: R, C++, C, Fortran
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: Samuel Roberts Noble Foundation, the National Science Foundation.
  • Contact: shizhong.xu _at_ | pzhao _at_
  • Collection: -


Zhang W, Dai X, Wang Q, Xu S, Zhao PX "PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies." PLoS Comput. Biol. 2016; 12(5):e1004925
PMID: 27224861
PMCID: PMC4880203

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