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PED file structure for CalculateGenotypePosteriors walker
I am analyzing exome data from a family with affected individuals in 3 generations. Thus, I have granparents-grandchilds relationships, cousins, etc... I tried to run calculate posteriors but the walker doesn't seem to be doing anything. I read somewhere in this forum that GATK walkers only accept trios. Is that true? If so, is there anyway to run this walker in a complex family representing several affected and unaffected individuals?
Thanks a lot in advance for your help