Extract individual samples from combined gvcf file

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Balat

• July 03, 2020 01:20

I am trying to use GenomicsDBImport to combine gvcf files for joint genotyping with GenotypeGVCFs. Looks like GenomicsDBImport requires individual gvcf files. I have several gvcf files from ten different runs which were combined with CombineGVCFs. Is there a way to extract individual gvcf files from the combined gvcf file to pass on to GenomicsDBImport?

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  Genevieve Brandt (she/her)

  • July 07, 2020 19:45

  Hi Balat, here is the documentation for CombineGVCFs: https://gatk.broadinstitute.org/hc/en-us/articles/360045253632-CombineGVCFs. You can use it instead of GenomicsDBImport before GenotypeGVCFs. When you use GenotypeGVCFs, you are able to input the combined multi-sample GVCF. You can read more about usage of GenotypeGVCFs here: https://gatk.broadinstitute.org/hc/en-us/articles/360045683331-GenotypeGVCFs

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