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Thursday, May 9, 2013

Create .ped and .map files from .vcf file

Here is a quick and easy script to convert .vcf files into a PLINK compatible .ped and .map file using vcftools.  Only bi-allelic loci will be output.  The --plink option can be very slow on large datasets in which case it is recommended to use the --chr option to output individual chromosomes or the --plink-tped option to output transposed PLINK files.

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