216
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→A. Convert doseage file into VCF format
=== 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 the tool from 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
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>
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]:
=== B. bgzip and tabix VCF files ===
=== B. bgzip and tabix VCF files ===
