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.

Friday, May 17, 2013

Download Region of Indexed VCF File

Tabix is a handy tool to download a region of interest from a .vcf file on an ftp site.  Below is an example of how to extract a region on chromosome 1 from a Complete Genomics .vcf file hosted on the 1000 Genomes ftp site.  The .vcf.gz file must have a matching .vcf.gz.tbi index file for tabix to work and the chromosome region of interest should not include "chr" with the chromosome number.

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