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How To Convert Vcf File To Plink Ped Format?

Hi! Biostar readers

This is my first post to Biostar,

I have a VCF file containing variants, i want to convert to PLINK PED format.

I have tried using, vcftools --vcf *.vcf --plink

But when i input this file into WGAViewer it says "SNP and p value cannot be the same", Why?

Is there any other software to convert vcf to plink ped format?

Thanks.

vcftools
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updated by Ram Ram • written by Ketan Padiya • Ketan Padiya

could you post some lines of the output that you obtain with your vcftools command?

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written by Pablo Marin-Garcia Pablo Marin-Garcia

5 answers

I have read that GATK has also a tool to do this conversion. It is called VariantsToBinaryPed. I have not used it yet but it looks useful and I will give it a try!

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updated by Ram Ram • written by Lídia • Lídia

Has anyone used this successfully? I tried, but it asks me for a metadata file with an extension of .fam. Given that I am trying to create this very file (i.e. .bim, .bed, and .fam) it confused me. I couldn't find a good article to explain how this works!

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updated by Ram Ram • written by HumeMarx • HumeMarx

I am still new to using PLINK and variant calling in general, so someone with more experience may correct me if needed. For my purposes I generally have a VCF file that I need to convert to PLINK for certain things. When I do this I manually create the .fam file for all my samples. I'm not sure of any other way as the information needed in the .fam file is not stored in the VCF file. It is meta information about your samples. This link here (https://www.cog-genomics.org/plink2/formats#fam) gives a good explanation of the .fam file format.

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written by alolex alolex

@alolex, Do you do this using the above mentioned tool from GATK VariantsToBinaryPed? Or with PLINK's --make-bed?

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written by gaelgarcia05 gaelgarcia05

Hello Ketan,

the vcftools 'plink' format is the ped ('pedigree') format that plink uses as primary INPUT. WGAViewer accepts the OUTPUT of plink (the association tests) and display you the pvalues in a genomic view.

A ped file (and its companion map file) does not contain any p-value. The p-values can be obtained doing the association test with plink (see the plink manual).

As you can see from the error you have "SNP and p value cannot be the same" WGAViewer wants a file with p-values not the ped files.

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written by Pablo Marin-Garcia Pablo Marin-Garcia

hello,i want to know how can i convert the hapmap genotypes data to plink format? i use peas first to convert to normal format and then to plink_in format. it creats several output files but without map file. BUt the pedsnp file seems to be the same with map file.

But when i load into plink, it turns out to be wrong with message:ped collume wrong.

so could any body tell me how to do this work?

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written by J.F.Jiang J.F.Jiang

Check out Plink 1.9 an alpha version of plink with VCF support.

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

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written by Thomas Johnson • Thomas Johnson

The Mega2 program can convert from VCF to PLINK format.

See: http://watson.hgen.pitt.edu/docs/conversions/vcf_or_bcf_plink.html

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updated by Ram Ram • written by dweeks.pitt • dweeks.pitt

You can work with VCFs in R.

To load the file use:

file='e:/d/genome/yourVCF.txt'
v <- read.table(file,sep='\t',header = T,fileEncoding="utf-16")
str(v)

The UTF-16 encoding was particularly hard to troubleshoot. Eventually Notepad++ helped me to detect this encoding problem.

It correctly ignores the header lines and detects column headers as well.

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updated by Ram Ram • written by user56 user56

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