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Old 11-29-2012, 04:30 PM   #1
Location: Malmö

Join Date: Sep 2008
Posts: 37
Default convert plink files to VCF


I would like to know if anyone has a script/tool to convert plink .map and .ped files into VCF.

We should have in mind that for instance a genotype in the .ped file could be AG, but this could correspond to the reverse strand (TC). Furthermore, it could be that the 1st allele is actually the alternative allele and the 2nd is actually the reference allele (according to the human reference genome), so it could have been GA.

Thanks in advance.
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