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== 2. Convert the minimac or Impute2 output into VCF format ==
== 2. Convert the minimac or Impute2 output into VCF format ==
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.
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.
Download and install the wrapper program here. [ PLEASE COMPLETE ]
Download and install the wrapper program here. [ PLEASE COMPLETE ]
<br>
To run the wrapper program, use the following command
To run the wrapper program, use the following command
<pre>> dose2vcf/dose2vcf --dose [ .dose file ] --info [ .info file ] --out [ output file prefix ]
<pre>> dose2vcf/dose2vcf --dose [ .dose file ] --info [ .info file ] --out [ output file prefix ]
</pre>
</pre>
For example, for imputed chromosome 1 data from FUSION:
For example, for imputed chromosome 1 data from FUSION:
<pre>> dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1
<pre>> dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1</pre>
</pre>
The expected output file is:
<pre>> out/FUSION.GWAS.1KG.imp.chr1.vcf</pre>
== 3. Prepare PED file for phenotypes and covariates ==
== 3. Prepare PED file for phenotypes and covariates ==
