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tumor normal pair

Dear GATK team,
I am a little bit confused about the Tumor Normal pair branch of GATK using haplotypecaller. We are recommended to re-align tumor sample and its normal control at the same time. As a result, a single re-aligned bam file will be created. But in the haplotypecaller step, it seems haplotypecaller prefers to input tumor and normal samples separately using independent -I. I just want to know the suggestion from GATK regarding the best approach to handle Tumor Normal pair analyses using haploypecaller. Shall I input co-realigned and recaliberated tumor normal bam with one -I? Does GATK perform somatic mutation filtering through tumor normal approach, or it is better if we do it by ourselves?
Thank you very much again!


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, you should NOT be using HaplotypeCaller for somatic calling. This tool is only intended for germline calling, and uses modeling algorithms that are completely inappropriate for somatic mutation calling. You should use MuTect or MuTect2 instead.

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