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EPACTS for DIAGRAM (view source)

Revision as of 21:21, 27 September 2012

480 bytes added ,  21:21, 27 September 2012
→‎2.  Convert the minimac or Impute2 output into VCF format
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== 2.  Convert the minimac or Impute2 output into VCF format  ==
 
== 2.  Convert the minimac or Impute2 output into VCF format  ==
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[ '''Explanation wrapper program usage ''']
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EPACTS requires input genotype / doseage information in VCF format.  After imputation with either minimac or Impute2, use this wrapper program "dose2vcf" to convert your doseage output to VCF format.
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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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Download and install the wrapper program here. [ PLEASE COMPLETE ]
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To run the wrapper program, use the following command
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<pre>&gt; dose2vcf/dose2vcf --dose [ .dose file ]  --info [ .info file ] --out [ output file prefix ]
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</pre>
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For example, for imputed chromosome 1 data from FUSION:
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<pre>&gt; dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1
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</pre>
    
== 3. &nbsp;Prepare PED file for phenotypes and covariates  ==
 
== 3. &nbsp;Prepare PED file for phenotypes and covariates  ==
Clement Ma
216

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