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# VCF contrasts - workflow

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

Tagged:

• Charlestown, MAMember Posts: 274 admin

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.

• Member Posts: 2

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.