Question: Using 1000 Genomes Vcf To Plink Conversion Script To Convert My Own Vcf Files?
gravatar for Click downvote
4.6 years ago by
Click downvote600 wrote:

I have a vcf file I'd like to convert from vcf to ped. Luckily, 1000 genomes has a perl script that can be used to do this:

Problem is, that script requires a -sample_panel_file, but I have no such thing. The VCF I have is from one population only and it is not from one of those in 1000 genomes. Does this mean I can't use this script to convert my own vcf file or what?

Or if I find the ids of the people in the vcf, can I just roll my own -sample_panel_file by making a file like

id1, population_name_i_made_up
id2, population_name_i_made_up

All advice appreciated.

Ps. I know vcftools has a vcf to ped converter but it does not play well with ubuntu thanks to ulim. I also know GATK has a tool to do this conversion, which I am attempting to get to work atm. If you know any other ways to convert vcf to ped (no matter how circuitous, please do tell me!)

vcf 1000genomes ped • 3.8k views
ADD COMMENTlink modified 4.6 years ago by Neilfws47k • written 4.6 years ago by Click downvote600

PSEQ reads in VCF and can output plink format.

ADD REPLYlink written 4.6 years ago by zx87544.3k

No, it only creates tped files (which vcftools also does swimmingly.) But upvote since I was too vague in the title.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Click downvote600

Use the new plink people:

ADD REPLYlink written 3.8 years ago by Click downvote600
gravatar for Neilfws
4.6 years ago by
Sydney, Australia
Neilfws47k wrote:

You can try the R package SNPRelate:

I say "should" since I have not tried the second function (I know that the first works fine).

ADD COMMENTlink written 4.6 years ago by Neilfws47k
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