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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 dosage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download the tool from here. If you used rs numbers during imputation, you can find mapping tables here
Use the wrapper program "dose2vcf" to convert your doseage output to VCF format. Download the tool from here. If you used rs numbers during imputation, you can find mapping tables here
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf
<pre>out/FUSION.GWAS.1KG.imp.chr1.vcf
</pre>
</pre>
Note that for longer chromosomes, the program is quite memory intensive. In this case, please convert dosages in shorter sections of the chromosome. For example, if the imputation was performed by sections, then convert these sections to vcf first, and then merge the vcf files together using vcftools [http://vcftools.sourceforge.net/docs.html#concat vcf-concat]:
Note that for longer chromosomes, the program is quite memory intensive. In this case, please convert dosages in shorter sections of the chromosome. For example, if the imputation was performed by sections, then convert these sections to vcf first, and then merge the vcf files together using vcftools [http://vcftools.sourceforge.net/docs.html#concat vcf-concat]:
