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Best practice using unifiedGenotyper to jointly call multiple genomes in a case-control project
Hi, GATK team
I have a project with 100s of WGS genomes contains unrelated case and control samples. I want to use the joint calling function in unifiedGenotyper to call all these genomes together and do VQSR afterwards. Here are my two questions:
Is there a best practice on this type of experimental design? Obviously, I cannot use the ped file to assign the case and control status because they are unrelated. Is there a way of putting that phonotypical data into the joint caller just like the ped file in family study setting?
If there is several phonotypical status based on the severeness of the disease instead of just case and control, is there a way to assign the phonotypical status something like extreme-case, mild-case, control, extreme-control? And what is the impact of giving the different shades of case-control status vs. Boolean case-control?
Thank you very much!!