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

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:

http://www.1000genomes.org/vcf-ped-converter#API%20Script

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!)

1000genomes vcf ped
• 7,193 views • link
updated by Ram Ram • written by Click downvote Click downvote

PSEQ reads in VCF and can output plink format.

• 138 views • link
written by zx8754 zx8754

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

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written by Click downvote Click downvote

1 answer

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).

• 270 views • link
updated by Ram Ram • written by Neilfws Neilfws

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