How To Convert .Ped To .Vcf File

Question

[cbm]

Hi,

I have tried using plink seq to convert a .ped file to a .vcf file. The result was completely wrong. I might have to write my own PERL script to do it, but thought I would ask if anyone has seen an available tool that would be able to do this. Thanks

[Zev.Kronenberg]

I have a PLINK to GVF conversion script. Maybe you could find a GVF to VCF script? Alternatively you could check out http://www.cmpg.unibe.ch/software/PGDSpider/

Answer 1

[Raony Guimarães]

Try this script

https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/plink_to_vcf.py

Or this

http://www.pypedia.com/index.php/Convert_PEDMAP_to_VCF_user_Kantale

[ivivek_ngs]

is it possible to use pypedia online? I want a tab delimeted file to convert to vcf format. The output is from fpfilter.pl . But how do I do it online? Just giving the path?

[Dan]

Note the new location of that script is here: https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/plink_to_vcf.py

Answer 2

[Kevin Blighe]

Updated answer: plink2 now has a --recode vcf option: https://www.cog-genomics.org/plink/1.9/data#recode