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Genotype refinement workflow for trio exome from GVCF
For a situation where one has only trio exome data, reaching the GVCF stage of GATK best practices, is there a way to do Genotype Refinement without doing joint genotyping? Because with only trio exome data, it is not possible to do joint genotyping (too few samples).
Alternatively, is it better to simply run HaplotypeCaller on the 3 exome BAM files together rather than using the GVCF approach?
Thanks for any advice.