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, 11:46, 18 September 2012
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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: |
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− | #<ref>Download and install EPACTS</ref> | + | #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 |
| #Run EPACTS association pipeline | | #Run EPACTS association pipeline |
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− | == 1. Download and install EPACTS == | + | == 1. Download and install EPACTS == |
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− | 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]. |
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| + | == 2. Convert the minimac or Impute2 output into VCF format == |
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| + | [ Explanation wrapper program usage ] |
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| + | An explanation of VCF files can be found [http://genome.sph.umich.edu/wiki/EPACTS#VCF_file_for_Genotypes here]. |
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| + | == 3. Prepare PED file for phenotypes and covariates == |