1000 Genome Phase 3 Variant Set Mirrors

The 1000 Genomes consortium has released their final release of the Phase 3 variant set. This is a set of phased called variants in thousand genome individuals. Data is available in compressed .vcf.gz format along with the indexed tabix files. Looking for a way to download the data. See these FTP sites:

US Mirror:
ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/

UK Mirror:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

The US 1000 Genomes mirror is substantially faster than the UK mirror when downloading files in the US.

How to Index a VCF File

There are two simple ways to create an index for a VCF file of sequence variants. The first is a command line driven approach using Tabix. For directions on installing Tabix, see this post. Here is the code needed for indexing the VCF file (either .vcf or .vcf.gz). First you need to make sure the vcf file is compressed as a vcf.gz file. This is done in the first line of code. Next, create a new .tbi index file in the same directory as your vcf.gz file. Using the -f command will write over an old index file that may be outdated or corrupted. The -p command will tell tabix to use the "vcf" file format.


The second way to index a VCF file is a point and click approach using the BROAD Institute's Integrated Genomics Viewer (IGV) program, a Java based program that will run on a variety of operating systems. To index a VCF file, open IGV, click on the Tools menu and select Run igvtools... A dialogue box will pop up. In the command drop down menu select Index and then click on Browse to select your desired .vcf file. Click run and a new .tbi index file will be created in the same folder.

There are probably other ways to index a VCF file, but these are the ones I am aware of. If you are aware of another method, please share in the comments.

Installing Tabix on UNIX

Tabix is an incredibly useful tool that indexes large .vcf files and makes it very efficient to find a particular genomic region in the file.  It is particularly useful for downloading small portions of files from publicly available ftp data repositories.  Here is a brief tutorial on how to install Tabix on a UNIX operating system.

(1) Go here to download the newest release.
(2) Extract the file:

(3) Compile the program by typing make on the UNIX command line.
(4) Export the path by adding the following line to your .bashrc file, saving your .bashrc file, and typing source on the UNIX command line.  Note: path_to_tabix is the directory where tabix is installed.

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.