I am trying to find a way to extract an arbitrary region of human genome from the 1000 genomes project's VCF files without having to download the genome or individual chromosome files up front, and ideally all from within R.
The closest functionality to what I have in mind is provided by the Ensembl DataSlicer (http://mart.ensembl.org/Homo_sapiens/Tools/DataSlicer?db=core), which is an online form. I would like to reproduce this functionality from within R, e.g. to programatically submit a bunch of regions,
and receive 3 VCF files with full 1kgp data (all populations, all SNPs) for these regions. Is this possible? As far as I can tell, I cannot do this without downloading the chromosome-level VCF files first (or the whole genome). I would love to be wrong here. Any ideas would be appreciated!