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HaplotypeCaller with Queue

flescaiflescai Posts: 67Member ✭✭
edited September 2012 in Ask the GATK team

Is there any example of a queue script calling variants with the HaplotypeCaller?

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,568Administrator, Dev admin
    Answer ✓

    Yes @ericminikel, that script can be adapted -to run HaplotypeCaller instead of UnifiedGenotyper. You may need to add some arguments to the argument collection, but it should be fairly straightforward.

    Geraldine Van der Auwera, PhD


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