The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
Last chance to register for the GATK workshop next week in Basel, Switzerland! http://www.sib.swiss/training/upcoming-training-events/training/gatk-workshop-lecture

VCF contrasts - workflow

AlmstrupAlmstrup Posts: 2Member

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:

Answers

  • CarneiroCarneiro Posts: 274Administrator, Dev 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.

  • AlmstrupAlmstrup Posts: 2Member

    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 Posts: 10,468Administrator, Dev admin

    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.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.