Question: how to find the haplotype info in population genomic databases
gravatar for CrazyB
4.3 years ago by
United States
CrazyB220 wrote:

How do I find the haplotype info from ExAC or 1000 Genomes?

1000 genomes states that their data released from phase 3 are all phased. But when I use the browser to find SNPs, I could not find much haplotype info of any of the SNPs that I am looking for

MacAurther Lab from the Broad Institute stated that they were working on providing haplotype info for data in ExAC. But as of now, I haven't seen any release that addresses the haplotype info.

If I have a handful of SNPs and would like to know in the population if any of them co-segregate in the same haplotype with any other known SNPs, how do I go about them without going through the whole VCF? Or is there any tool that can help me search for that info?

Thanks a lot.

exac haplotype 1000genomes • 2.0k views
ADD COMMENTlink modified 4.3 years ago by Denise CS5.1k • written 4.3 years ago by CrazyB220
gravatar for Denise CS
4.3 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

Perhaps the Transcript haplotype in Ensembl could give you some clues? If not, have a look at the Linkage disequilibrium (LD) and Linkage Disequilibrium Data pages. Those are all based on 1000 Genomes data only. As for the Exac data, it may not be available yet. In one of their blog posts (A Guide to the Exome Aggregation Consortium (ExAC) Data Set), they seem to mention something about the HaplotypeCaller but nothing else AFAIK. You may want Tweet Daniel. He will confirm or deny that.

ADD COMMENTlink written 4.3 years ago by Denise CS5.1k

Thanks ! Ensembl database does have the info.

ADD REPLYlink written 4.3 years ago by CrazyB220
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