I am looking for an efficient way to get 1000 Genomes data for ~70k dbSNP ids. (I am primarily interested in putative impact and allele frequencies.)
Is there a convenient way to do this?
A good solution would be some way to query 1000 Genomes programmatically and in bulk (as opposed to one dbSNP id at at time), but I have not found it yet.
Another possibility would be do download files from 1000 Genomes that I can process locally, but I have not been able to locate a reasonably-sized download that has the information I'm looking for. I could download all of ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502, but that could take a long time, and pretty much fill up my hard disk, without any guarantee that what I'm looking for is in that massive download.
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written
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kynnjo •
2 answers
The following java program should do the trick:
Thought to give a quick answer as this thread will likely get a fair bit of traffic in the future.
If you follow steps 1-3 of my tutorial, here: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format, then you'll have the data in BCF format. On my disk, the entire 1000 Genomes data (phased genotypes) in a single BCF file occupies 8.3 gigabytes. I interrogate it frequently for diverse projects.
Kevin
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Title of this post can be refined to indicate your exact requirement.
You know how to get the data in bulk but you are looking for an efficient way to just get the data for 70k dbSNP id's that you want. Is that correct?
If you are able to use Amazon AWS then the data is available there and won't require a download.