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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

VCF contrasts - workflow

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?



  • CarneiroCarneiro Charlestown, MAMember

    I am not sure I understand what you want to do, but it seems to me like you are talking about the Plink tools ? You can make queries in the GATK on vcfs using SelectVariants, VariantEval, GenotypeConcordance, CombineVariants and other tools.

  • Well, lets say I want to group my vcfs in high and low BMI, high and low LDL etc. and look for the SNVs that differentiate the groups.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    That is definitely something you can do with VariantEval and GenotypeConcordance. Those tools have a lot of capabilities, you should look them up in the documentation.

    We don't currently provide a set workflow for this type of analysis because it there are so many possible variations depending on your study design.

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