Hi

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?

Thank You