Question: How to create map file for synthetic genome data?
gravatar for jody.xha
6.6 years ago by
European Union
jody.xha0 wrote:


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

plink • 1.8k views
ADD COMMENTlink written 6.6 years ago by jody.xha0

This post might be relevant. Any Recommendation On Program That Could Simulate Gwa Case/Control Data ?

ADD REPLYlink written 6.5 years ago by zx87549.9k
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