I realized that the current hapmap (hapmap_3.3.hg19.vcf) and 1000G omni (1000G_omni2.5.hg19.vcf) bundle files contain only sites, not genotypes. Are the corresponding VCF files with genotypes available for download?
Done -- all sites-only files have been renamed accordingly.
We don't provide them, but you should be able to get them from the HapMap and 1000G project websites.
Thanks for your quick response. I remember an earlier version of the bundle used to have them...
Hmm, we probably changed that to cut down on the file size.
I can see that. The two files would be close to 50G in total. It just the naming is a little confusing now. The site only version used to be called "hapmap_3.3.hg19.sites.vcf" so I assumed the current one has genotype, until I tried to find them.
Ah, sorry about that, you're right. I'll see if we can fix the names.