I created 400 or so gvcf files (g.vcf.gz) using the gatk HaplotypeCaller. These files show populations for three distinct traits (HR, MR, HS). Now, I want to use gatk GenomicDBImport to combine gvcfs from various samples. Should I use this tool on all 400 samples, or should I use it on each phenotype population (HR, MR, HS) separately?



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