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EPACTS requires input genotype / doseage information in VCF format. From minimac or Impute2, you wil start with your imputed dosage file.
EPACTS requires input genotype / doseage information in VCF format. From minimac or Impute2, you wil start with your imputed dosage file.
=== A. Convert doseage file into VCF format ===
=== A. Convert doseage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download and install the wrapper program here. [ PLEASE COMPLETE ]
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download and install the wrapper program here.'''[ PLEASE COMPLETE ]'''
To run the wrapper program, use the following command
To run the wrapper program, use the following command
<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>> dose2vcf/dose2vcf --dose FUSION.GWAS.1KG.imp.chr1.dose --info FUSION.GWAS.1KG.imp.chr1.info --out out/FUSION.GWAS.1KG.imp.chr1</pre>
The expected output file is:
The expected output file is:
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf</pre>
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf</pre>
=== B. bgzip and tabix VCF files ===
=== B. bgzip and tabix VCF files ===
