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Using Plink to test 1000 human Genome population data distance, most recent common ancestor and time since divergence

Hi everyone,

I'm trying to use vcf files from the 1000 Human Genomes Project to establish distance between populations, most recent common ancestor and a timeline showing when the populations diverged - all to be shown in a phylogenetic tree.

I'm very new to bioinforatics and am told using a program like Plink is best for a non-programmer such as myself.

Does anyone have experience with this kind of operation and would you be able to tell me how to get started? I have the VCF files but I'm not sure how to use them in Plink.

Thanks in advance for any help!

plink 1000 human genomes vcf
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written by lyle • lyle

1 answer

First of all, study the documentation:

http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-doc-1.07.pdf

It's a little bit old, but it will give you some ideas:

http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml

There are many posts in biostars.org about plink, just go to

https://www.biostars.org/ and type 'plink' and whatever else you want to know.

Here is a useful list of updates,

https://www.cog-genomics.org/plink2

"the following documented PLINK 1.07 flags are not supported by 1.90 beta 3"

This is the example of plink-usage:

A: 1000Genomes To Haploview

Look at this link below, it seems to be useful to you:

https://psychgen.u.hpc.mssm.edu/plinkseq/tutorial.shtml

See also these biostars.org posts:

this one:

Using 1000 Genomes Vcf To Plink Conversion Script To Convert My Own Vcf Files?

and this one:

PLINK and 1000 Genome browser

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written by natasha.sernova natasha.sernova

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