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Merged VCF file

Merged VCF file

Gencove supports generating a merged VCF file containing variant calls from all successful and available (i.e., not archived) samples in a project.

Generating a merged VCF file is initiated from the Gencove Dashboard, by opening a project and clicking the "Merge VCFs" button. Once the merge operation is complete, a download button will appear on the project page.

Please keep in mind:

  • merging is only possible for projects with two or more successful and available (i.e., not archived) samples
  • not all project configurations support merging
    • in case you need a merged VCF and a project configuration you are using does not support it, please let us know at
  • depending on the number of samples in your project, merging may take anywhere between several minutes and several hours
  • if multiple samples have the same client_id, the merged VCF file will only contain the newest sample
  • if a subset of samples in the project are archived, they will not be added to the merged VCF. To include them in the merged VCF, restore the samples first.

In addition to the web interface, the following CLI commands can be used to access merged VCF functionality:

Creating a merged VCF

A merged VCF file can be created using the gencove projects create-merged-vcf command.

$ gencove projects create-merged-vcf <project-id>

Checking the status of a merged VCF

Status of the merging job can be checked using the gencove projects status-merged-vcf command.

$ gencove projects status-merged-vcf <project-id>

Downloading the merged VCF

The merged VCF file can be downloaded using the gencove projects get-merged-vcf command. Optionally, --output-filename my-filename can be used to override the default filename.

$ gencove projects get-merged-vcf <project-id>