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VCF contrasts - workflow

AlmstrupAlmstrup Member Posts: 2

I am just starting with GATK but even though I have looked and looked I can not find a simple walkthrough of having many VCFs and running a range of contrasts based on sample data. I guess this must be one of the most common used tools.
I have 200 VCFs that I want to contrast in many different ways depending on sample phenotype.
Is there anyone that can direct me to a good guide on how to do that?
Thanks

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