Changes

= Motivation and Rationale  =

= Motivation and Rationale  =

EPACTS is a software pipeline developed to perform various statistical tests for analysis of whole-genome / whole-exome sequencing data.  The main motivation for using EPACTS is to use a consistent analysis framework for association analysis in the DIAGRAM consortium.  In addition, for analysis of low frequency variants (minor allele frequency [MAF] < 5%), standard logistic regression Wald or likelihood ratio tests found in existing association software are conservative or anti-conservative respectively.  We implemented two statistical tests recommended for analysis of low frequency variants: (1) logistic regresion-based score test and (2) Firth bias-corrected logistic regression [http://www.stat.duke.edu/~scs/Courses/Stat376/Papers/GibbsFieldEst/BiasReductionMLE.pdf (Firth, 1993)].  For analysis of common variants, any asyptotic logistic regression test has well-controlled type I error rates and asymptotically equivalent power.  For simplicity and consistency, we propose the use of both score and Firth tests for testing all allele frequencies.  

[[EPACTS|EPACTS]] is a software pipeline developed to perform various statistical tests for analysis of whole-genome / whole-exome sequencing data.  The main motivation for using EPACTS is to use a consistent analysis framework for association analysis in the DIAGRAM consortium.  In addition, for analysis of low frequency variants (minor allele frequency [MAF] < 5%), standard logistic regression Wald or likelihood ratio tests found in existing association software are conservative or anti-conservative respectively.  We implemented two statistical tests recommended for analysis of low frequency variants: (1) logistic regresion-based score test and (2) Firth bias-corrected logistic regression [http://www.stat.duke.edu/~scs/Courses/Stat376/Papers/GibbsFieldEst/BiasReductionMLE.pdf (Firth, 1993)].  For analysis of common variants, any asyptotic logistic regression test has well-controlled type I error rates and asymptotically equivalent power.  For simplicity and consistency, we propose the use of both score and Firth tests for testing all allele frequencies.  

= Outline of analysis protocol  =

= Outline of analysis protocol  =

This is the analysis protocol for analysis of imputed DIAGRAM datasets using the EPACTS pipeline.  We assume that your dataset has been imputed using [[Minimac|minimac]] or I[[IMPUTE2|mpute2]].  Starting with minimac or impute2 output:

This is an overview of the analysis protocol for analyzing imputed DIAGRAM datasets using the EPACTS pipeline.  We assume that your dataset has been imputed using [[Minimac|minimac]] or I[[IMPUTE2|mpute2]].  Starting with minimac or impute2 output: