How would I go about getting 1000 Genomes frequencies for
variants described in hg18 coordinates?
you could download the data from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20100804/ (build 37/hg19) and then process it with liftOver ?
liftover for snps is tricky, you are better getting flanking sequences and mapping between the 2 assemblies IMHO
You can take the snps from the pilot of course which already are in NCBI36/HG18
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