Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.

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.

1 comment: