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mutect2 on Multiple matched samples onGATK4.1.3

dara_mimsdara_mims Montreal, CanadaMember

I was wondering if it is possible to perform somatic variant calling on multiple matched samples in version 4.1.3, since it only takes in the name of the normal sample, how is the program able to match the right normal with the right tumor sample? If it isn't able to do that, is it possible to combine all vcf files output by mutect2 since CombineVariants has been disabled? Thank you.

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