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Accessing population specific mutation data from 1000 genome.

I am trying to download mutation data from 1000 genome. I am interested in white/not Hispanic or Latino population for the study. I have a few questions regarding the data.

  1. From the mentioned category on the 1000 genome (http://www.internationalgenome.org/faq/which-populations-are-part-your-study/) I think CEU is the best suited for my study.

  2. With the above assumption, I download VCF files from http://www.internationalgenome.org/data-portal/sample/NA06985. In the VCF files, they have categorization based on super-population only (for CEU it is EUR). But EUR is not exclusive to CEU. So, Is there a way or other metadata I missed so that I can filter mutations only for CEU from the VCF files?

1000gnome vcf mutation
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updated by Kevin Blighe Kevin Blighe • written by prashant10991 • prashant10991

1 answer

Yes, you would mainly want the following EUR populations, i.e.:

  • CEU, Utah Residents (CEPH) with Northern and Western European Ancestry
  • TSI, Toscani in Italia
  • GBR, British in England and Scotland

The others are:

  • FIN, Finnish in Finland
  • IBS, Iberian Population in Spain

People from Iberia are obviously hispanic. People from Finland have been shown to be statistically significantly distinct from the other European populations.

On your point 2, there is indeed a better metadata file. Take a look at #Step 2, here: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

Kevin

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written by Kevin Blighe Kevin Blighe

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