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PCA plot using exome-seq data VCF and 1000Genomes data

Dear all,

I would like to check the ancestry of several individuals for which I have individual VCF files. The VCF files are based on b37.

I would like to run principal component analysis to confirm overlap with individuals of Caucasian ancestry included in 1000Genomes and plot my results. Any idea how I could do this?

Thanks very much.

vcf 1000g pca
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written by VasGene • VasGene

I'll close this post because it is duplicated. We prefer to have the answers concentrated in the same discussion. The other post is old, but some of the answers are recent and valid (e.g. plink with vcf, SNPrelate)

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Hello VasGene!

We believe that this post does not fit the main topic of this site.

I'll close this post because it is duplicated. We prefer to have the answers concentrated in the same discussion. The other post is old, but some of the answers are recent and valid (e.g. plink with v

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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