PEPIS: A Pipeline for estimating EPIStatic effect in Quantitative Trait Locus Mapping and Genome-Wide Association Studies   
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Module Description

  • PEPIS include four function modules: 1) kinship matrix calculation(km_calc), 2) poygenic component analysis(pg_anal), 3) genome scanning for main genetic effect(gs_main), 4) genome scanning for epistatic genetic effect(gs_epis).
  • PEPIS need the additive and dominance genotypic data files as the inputs to calculate the 6 polygenic kinship matrices, and furthermore need the phenotypic data file to estimate the polygenic component ratios and genome scanning for main and epistatic genetic effects.
  • All of the function modules are developed in C++ and have been successfully compiled and tested in our linux system. User can freely download, modify and compile the source code without restriction into their own pipeline.


Test Dataset

Source Code

  • All of the source code have been archived into a package and can be downloaded from PEPIS_Source_Code

Matlab Scripts for PolyGenic Effect Illustration

Build and Run

  • tar -xf ./PEPIS_Source_Code.tar
  • cd PEPIS_Source_Code/gs_epis
  • make clean
  • make
  • cd ../gs_main
  • make clean
  • make
  • cd ../km_calc
  • make clean
  • make
  • cd ../pg_anal
  • make clean
  • make

Development Information

Current Version:V1.0
Licence:GPL 3.0
Last Update:07/21/2015
Contact:Wenchao Zhang, wezhang AT

Copyright © The Zhao Lab