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Combine gvcf files generated with GATK and Isaac

AdemirAdemir TurkeyMember

Hi. I have a batch of g.vcf files generated with IsaacVariantCaller. I also have another batch generated with GATK HaplotypeCaller. I want to combine these to batches to perform GenotypeGVCFs. Is there any way to combine these two batches? I do not have BAM files of the samples generated with Isaac, so I can't start from that step. Thank you in advance.



  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Ademir

    CombineGVCFs: Merges one or more HaplotypeCaller GVCF files into a single GVCF with appropriate annotations

    So no, it is not possible to combine these to batches to perform GenotypeGVCFs.

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