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merging bam files for an individual

eflynn90eflynn90 Washington DCMember

I'm running HaplotypeCaller in GVCF mode, followed by GenotypeGVCF. For some individuals, I have more than one aligned bam file. Do I need to combine the individual's bam files in HaplotypeCaller to produce one GVCF, or can I produce multiple GVCFs per individual and combine them in GenotypeGVCF?

Thanks.

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