Hi all! I'm having problems with the input files for running GERMLINE (ibd sharing).
I have a VCF file with phased data for chromosome 22. I converted it to ped/map files using ./impute_to_ped from GERMLINE package. Even though, the analisis was interrupted by a server error.
So, I'm thinking trying with GERMLINE2, but the input files requiered are haps file, sample filea and genetic map file. How do I get this files from de VCF file that I already have?
Please I need help with this, is the first time that I worked with this type of data.