1000 Genomes Base-By-Base Frequency On Hg18

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

Thanks!

genome hg dbsnp

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updated 15.1 years ago by Pierre Lindenbaum

• written 15.1 years ago by Archie •

1 answer

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 ?

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written 15.1 years ago by Pierre Lindenbaum

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/

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written 15.1 years ago by Laura

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