Question: Using Plink to test 1000 human Genome population data distance, most recent common ancestor and time since divergence
gravatar for lyle
2.6 years ago by
lyle0 wrote:

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!

1000 human genomes plink vcf • 918 views
ADD COMMENTlink written 2.6 years ago by lyle0
gravatar for natasha.sernova
2.6 years ago by
natasha.sernova3.1k wrote:

First of all, study the documentation:

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

There are many posts in about plink, just go to and type 'plink' and whatever else you want to know.

Here is a useful list of updates,

"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:

See also these 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

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by natasha.sernova3.1k
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