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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:
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:
#Download and install EPACTS
#Download and install EPACTS
#Convert the minimac or Impute2 output into VCF format
#Convert the minimac or Impute2 output into VCF format
#Prepre PED file for phenotypes and covariates
#Prepre PED file for phenotypes and covariates
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here].
EPACTS is available for download [http://www.sph.umich.edu/csg/kang/epacts/download/index.html here].
== 2. Convert the minimac or Impute2 output into VCF format ==
== 2. Convert the minimac or Impute2 output into VCF format ==
[ Explanation wrapper program usage ]
[ Explanation wrapper program usage ]
An explanation of VCF files can be found [http://genome.sph.umich.edu/wiki/EPACTS#VCF_file_for_Genotypes here].
An explanation of VCF files can be found [http://genome.sph.umich.edu/wiki/EPACTS#VCF_file_for_Genotypes here].
== 3. Prepare PED file for phenotypes and covariates ==
== 3. Prepare PED file for phenotypes and covariates ==
EPACTS accepts the PED format supported by MERLIN or PLINK to represent the phenotypes and covariates. You may prepare either (1) a PED file without column headers + accompanying DAT file, or (2) a PED file with column headers.
