Variant Annotator of a multisample vcf, how to set the bam files in the args
Posted in Ask the GATK team | Last updated on

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I have a vcf containing multiple samples. I would like to put the bam files also as input for the Variant Annotator but how does the variant annotator know which bam is for wich column in the vcf? Does the order of the args of the bam files need to correspond to the order of the samples columns in the vcf?



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