CODEWITHSUNDEEP
bioinformaticsvcftoolsvcf-variant-call-format
NeverBe
NeverBe

Reputation: 107

How to convert vcf file to ped file using plink?

I am trying to convert a .vcf file to a .ped file using plink. I have read some manuals and posts online, but it seems that no one specifically mentions how to convert vcf to ped.

I am hoping that there may be some experts here who have experience with plink to convert vcf to ped. I would appreciate it if you could share the knowledge. Moreover, if there is another way (non-plink) of doing that, please do share it.

Thank you!

Upvotes: 6

Views: 21227

Answers (2)

Ophiothrix
Ophiothrix

Reputation: 821

Plink provides its own functionality for converting vcf (and other format) files to plink-compatible ones. The command you're looking for is recode and the actual command would look like this:

plink --vcf myfile.vcf.gz --recode --out myfile

Upvotes: 8

Will Pitchers
Will Pitchers

Reputation: 76

I convert my vcf files to PLINK formats (ped, fam, map) using VCFtools: https://vcftools.github.io/man_latest.html

My commands look like this:

vcftools --vcf my_data.vcf --out my_data --plink

Upvotes: 6

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