Angie Mosquera, Software Engineer - Mar 21, 2023

User-customizable project configurations

At Gencove, our goal is to achieve the universal application of genomics by continuously expanding the customizability and accessibility of our platform. To provide our users with greater control over their projects, we are pleased to announce a new feature that allows users to customize project configurations on the Gencove platform.

This means users can now select from the following customization options when creating new projects:

  1. Disable all quality control - By default, Gencove imputation pipelines have various quality controls to ensure samples are compatible with their assigned pipeline. Disabling QC turns off these controls. These include:
    • De-duplicated sequencing depth of at least 0.1x
    • Contamination fraction of no more than 0.06
    • At least 6% of SNPs in the reference panel identified
  2. Enable leave-one-out (i.e. "autoskip") analysis - Leave-one-out analysis is a pipeline modification used to validate reference panel performance by excluding known samples from the reference panel, and using these excluded reference panel haplotypes as truth data for calculating concordance of imputed haplotypes.

Configuration details

In addition to the new feature, the web interface now provides users with more information about the configuration used to process their samples. This includes a description of the configuration, information about the reference and imputation datasets, and parameter values used in the configuration.


Customizing a project configuration is as simple as creating a project on the Gencove system with the relevant modifications. The following example shows how this is done using the web interface.

Select the desired configuration and choose any combination of the checkboxes available under “Advanced Configuration”.

Once you have filled out the project name and description, press the "Add new project" button at the bottom of the page to complete the action. You will now be able to add samples to your project to be processed with your modified configuration.

More information on how to customize project configurations is available in the Gencove Knowledge Hub, and as always, let us know what you think.