Can I get genotypes for a specific individual/population from VCF files?

Either the Data Slicer or using a combination of tabix and VCFtools allows you to sub sample VCF files for a particular individual or list of individuals.

The Data Slicer, described in more detail in the documentation, has both filter by individual and population options. The individual filter takes the individual names in the VCF header and presents them as a list before giving you the final file. If you wish to filter by population, you also must provide a panel file which pairs individuals with populations, again you are presented with a list to select from before being given the final file, both lists can have multiple elements selected.

To use tabix you must also use a VCFtools Perl script called vcf-subset. The command line would look like:

tabix -h 17:1471000-1472000 | perl vcf-subset -c HG00098 | bgzip -c /tmp/HG00098.20100804.genotypes.vcf.gz

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