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Identify Compound Heterozygotes Using Select Variants

sboylesboyle Posts: 22Member

Hello Team,

Is there a best practice for finding compound heterozygotes using GATK? I can easily find recessive pattern variants using the SelectVariants tool, however, I have not been able to find a way to select compound hets. I am sure the Broad has a straightforward way. Is it somehow integrated into the GATK tool set?

I have considered using something like Gemini, but I would prefer to keep tools use to fewer product lines whenever possible.

Thanks for your help! Sean


  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,192Administrator, GATK Developer admin

    Hi Sean,

    Sorry to answer you so late. We have a little internal debate going on here about exactly what is meant by a compound het (it seems to mean different things to different people): are you thinking of two het sites side by side (which would be a phasing issue), or cases where you have both alleles mutated, so if REF is A, you're T/G?

    Geraldine Van der Auwera, PhD

  • sboylesboyle Posts: 22Member

    Hello Geraldine,

    In my case I'm interested in identifying when the gene copy from a mother contains damaging mutation A and the gene copy from the parent contains damaging mutation B. The parents in this case would be heterozygous for their own mutations and could be haplosufficient. The affected child however, would have two damaging copies and disease state. These mutations could either be at the same site (Such as in your second case) or what I believe you are referring to in your first case. I think phasing would be good here, but ultimately if you can pair up Damaging mutation A in only one parent and child and damaging mutation B in only one parent and child that would be sufficient to make the call. Some tools such as the ingenuity suite claim to be able to do this, however I would much prefer to stay with your suite. I was hoping that select variants could be used for this type of (If one from parent A and Child and other from parent B and child then output) situation.

    Thank you for your suggestions! Sean

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,192Administrator, GATK Developer admin

    Oh I see, thanks for the clarification. Unfortunately we don't have anything built-in to find such cases. We don't have the resources to add this right now, but it wouldn't be too difficult to write a tool to do this. We'd be happy to look at an external contribution if you or somebody else were to write it.

    Geraldine Van der Auwera, PhD

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