I have a vcf file I'd like to convert from vcf to ped. Luckily, 1000 genomes has a perl script that can be used to do this:
Problem is, that script requires a -sample_panel_file, but I have no such thing. The VCF I have is from one population only and it is not from one of those in 1000 genomes. Does this mean I can't use this script to convert my own vcf file or what?
Or if I find the ids of the people in the vcf, can I just roll my own -sample_panel_file by making a file like
id1, population_name_i_made_up id2, population_name_i_made_up ...
All advice appreciated.
Ps. I know vcftools has a vcf to ped converter but it does not play well with ubuntu thanks to ulim. I also know GATK has a tool to do this conversion, which I am attempting to get to work atm. If you know any other ways to convert vcf to ped (no matter how circuitous, please do tell me!)