4 months ago by
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.