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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!