1000 Genomes Base-By-Base Frequency On Hg18

Question

[Archie]

How would I go about getting 1000 Genomes frequencies for variants described in hg18 coordinates?

Thanks!

Answer 1

[Pierre Lindenbaum]

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 ?

[Laura]

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

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/paper_data_sets/a_map_of_human_variation/