Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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.

Tagged:

Answers

  • 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.

Sign In or Register to comment.