How To Convert Vcf File To Plink Ped Format?

Question

[Ketan Padiya]

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.

[Pablo Marin-Garcia]

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

Answer 1

[Lídia]

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!

[HumeMarx]

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!

[alolex]

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.

[gaelgarcia05]

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

Answer 2

[Pablo Marin-Garcia]

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.

[J.F.Jiang]

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?

Answer 3

[Thomas Johnson]

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

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

Answer 4

[dweeks.pitt]

The Mega2 program can convert from VCF to PLINK format.

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

Answer 5

[user56]

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.