Hi all,

I have a list of more than 100 SNPs (rsXXXXXX) and I would like to obtain the different allele frequencies that each of them shows in each of the 1000Genomes populations (if possible not manually...). Is there any tool, R package etc, that allows to download them all at once?
I've thought that I could maybe obtain those frequencies from the UCSC database or directly from the 1000Genomes database, but I'm open to any suggestions.
Thank you very much in advanced!
Solution 1: The raw variant call data can be downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ .  Once you have those files, the INFO column in each VCF file contains superpopulation allele frequencies, and there are a bunch of tools which can look up the INFO column entry for a particular rsID.  The one complication is that, since there's a separate VCF file per chromosome, you may first need to figure out which rsIDs are on which chromosomes.

Solution 2: With plink 2.0, http://www.cog-genomics.org/plink/2.0/resources#1kg_phase3 provides a single merged dataset containing all chromosomes (download the boldfaced links, then rename phase3_corrected.psam to all_phase3.psam).  Then,

    plink2 --pfile all_phase3 vzs --extract [your list of rsIDs] --export vcf

can then be used to export a VCF with only the rsIDs you care about; the precomputed superpopulation allele frequencies will be in the INFO column of this freshly generated VCF.  You can also define your own populations with --keep and compute allele frequencies on the fly with --freq.