The Data Slicer provides an interface which allows users to get subsections of either VCF (VCFtools) or BAM (SAMtools) files based on genomic coordinates.
Currently available for GRCh37 only, you can access the Data Slicer from the tools link in the menu bar at the top of every page.
Firstly, you have the option of naming your job.
Then you will need to select the file format, VCF or BAM.
To select the region you want to slice from, type the chromosome and coordinates; e.g. 1:1-50000.
If you chose VCF as your format, you will be given the option to select 1000 Genomes Phase 3, 1000 Genomes Phase 1 or to provide a URL. For BAM you only have the option to provide a publicly visible URL. These URLs must be accompanied by either a tabix index (.tbi) or BAM index (.bai) of the same name. All 1000 Genomes VCF and BAM files on the FTP site have these indices with them. Please note that this service will only work for other BAM files over http.
If you are slicing a VCF file you can also subset the data by individual or population. You can either put a comma separated list of individuals or populations in the box or select individuals or populations from the dropdown list. If you wish to select multiple individuals or populations, hold the ctrl key (on Windows/Linux) or the cmd key (Macs).
After clicking next the system produces your final file.