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
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
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?
Note the new location of that script is here: https://github.com/chapmanb/bcbio-nextgen/blob/master/scripts/utils/plink_to_vcf.py
Updated answer: plink2 now has a --recode vcf option:
https://www.cog-genomics.org/plink/1.9/data#recode
Log in to answer this question.
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/