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

Question

[lyle]

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!

Answer 1

[natasha.sernova]

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