How to convert vcf file to ped file using plink?

Question

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!

score 7 · Answer 1 · answered Sep 05 '18 at 16:57

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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

answered Sep 05 '18 at 16:57

Ophiothrix

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score 6 · Accepted Answer · edited May 15 '18 at 16:14

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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

edited May 15 '18 at 16:14

zx8754

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answered Oct 17 '16 at 16:08

Will Pitchers

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Usually works, however it fails with polyploid data (if they are flagged as such by e.g. freebayes variant caller). – jena Sep 22 '17 at 13:08
How does `vcftools` generate the .fam / .ped files if it doesn't take pedigree info as input? – Carmen Sandoval May 09 '18 at 03:29
My guess is that is populates those fields with default values. – Ophiothrix Sep 05 '18 at 16:52

How to convert vcf file to ped file using plink?

2 Answers2