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Genotype refinement workflow for trio exome from GVCF

GERGER Member
edited November 2019 in Ask the GATK team

Hi,
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.

Post edited by GER on

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