How do I get a sub-section of a vcf file?

Answer: 

There are two ways to get subsections of our VCF files.

The first is to use the Data Slicer tool from our browser which is documented here. This tool gives you a web interface requesting the url of any vcf file and the genomic location you wish to get a sub slice for. This tool also works for BAM files. This tool also allows you to filter the file for particular individuals or populations if you also provide a panel file.

The second method is using tabix on the command line. e.g 

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz 2:39967768-39967768

The VCF format and a c++ and perl tool set for vcf files can be found at vcftools on sourceforge

Please note all our vcf files using straight intergers and X/Y for their chromosome names in the Ensembl style rather than using chr1 in the UCSC style. If you request a subsection of a vcf file using a chromosome name in the style chrN as shown below it will not work.

  tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz chr2:39967768-39967768