Gencove supports generating a merged VCF file containing variant calls from all successful and available (i.e., not archived) samples in a project.
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 by submitting a support ticket request.
- 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.
Ways to download a merged VCF
There are a few ways to download a merged VCF.
Generating a merged VCF file can be initiated from the Gencove Platform. Once you have successfully signed in to your account, you will automatically be directed to the “My Projects” tab view.
On this page, you can select the project name of which you wish to create a new merged VCF file.
After selecting the correct project, scroll toward the bottom of the page until you see the header titled “Project Samples”. It is in this section where you can see the sample(s) that succeeded and failed QC.
Note: you can only download data from samples that have a green "Succeeded" status.
After reviewing the success/failures, and you're ready to merge, click on the blue button located on the right side of the screen labeled "Merge all VCF files"
Once the merge operation is complete, a gray outlined button labeled "Download Merged VCF" will appear underneath the "Merge all VCF files" button on that project's page. Click on the gray outlined button to download you merged VCF files.
In addition to the web interface, the following CLI commands can be used to access merged VCF functionality:
To learn more about merging VCF files using the API, click here for the API Reference.
You'll want to pay particular attention to the commands under the project header.