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EPACTS for DIAGRAM

7 bytes removed, 10:05, 2 February 2017
A.  Convert dosage file into VCF format
=== A.  Convert dosage file into VCF format ===
Use the wrapper program "dose2vcf" to convert your doseage output to pseudo VCF format.  Download the tool from [http://wwwcsg.sph.umich.edu/csg/cfuchsb/dose2vcf_v0.5.gz here]. If you used rs numbers during imputation, you can find mapping tables ready for dose2vcf [http://wwwcsg.sph.umich.edu/csg/cfuchsb/mapping_rs_ALL.GIANT.phase1_release_v3.20101123.tgz here (214 Mb) ]
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Note that for longer chromosomes, the program is quite memory intensive. &nbsp;In this case, please convert dosages in shorter sections of the chromosome. &nbsp;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. &nbsp;bgzip and tabix VCF files ===
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