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=== 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 the tool from here.
If you used rs numbers during imputation, you can find mapping tables here
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 ===
