We have generated genome data from a simulation and would like to analyse it with plink.
I have built an output module which creates a ped file, but some questions remain..
The first question is: what should i use for the 'phenotype ' value in the ped file?
Currently, i set it to 1 ('unaffected') - is that OK?
The second question is about the map file.
Since our genomes do not reside on any chromosomes and do not have a base pair position on the human genome, i don't know how to create a map file for our data.
Do you have a suggestion how i should proceed?