how to delete some GVCFs from GATK GenomicsDBImport?

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how to delete some GVCFs from GATK GenomicsDBImport? #8114

Open JingChunSun opened 1 year ago

JingChunSun commented 1 year ago

I have combined some GVCFs by GenomicsDBImport, and continuity added other samples. however, I find some mistakes with previous samples, how to delete these samples from GATK GenomicsDBImport?

droazen commented 1 year ago

@mlathara @nalinigans Does GenomicsDB currently support deletion of samples?

mlathara commented 1 year ago

It is not possible to delete samples from a GenomicsDB workspace.

It is possible to add some support where things like query tools like GenotypeGVCFs can optionally specify a list of samples that they want queried from the workspace.

JingChunSun commented 1 year ago

Thanks for your help, is it possible to replace the previous wrong GVCF by adding the GVCF with the same sample ID to GenomicDB?