After utilization or gaining more insight into configuration details, your team has decided to slightly modify one of Gencove's configuration pipelines. Users now have greater control over their projects and can complete this action themselves.
First step in modifying configurations is to create a new project. Please note: these customizations are only available for new projects and cannot be changed after the project has been created. Additionally, if your project had a private configuration with one of these modifications and you would like to process more samples using a modified configuration, a new project must be created.
Read our related Resource Hub article for more information on how to create a new project.
How to modify a pipeline configuration?
The following customizations are available for project configurations during project creation:
- 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
- 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 the imputed haplotypes. Feel free to contact us should you need assistance.
Modifying pipeline configurations on the Gencove Platform
While creating your new project, you can click on any of the listed configurations to view their details. The details will appear in a grey box located in the top right corner of the page. You will be able to see a description of the configuration, as well as two expandable sections.
- The first expandable section is named "Configuration details." It provides information about the reference and imputation datasets, as well as some of the parameter values used in the configuration.
- The second expandable section is named "Advanced Configuration". It contains two checkboxes for each customization configuration.
You can select any combination of the two customization options. Once you have filled out the project name and description, click the blue "Add new project" button at the bottom of the page to complete the action. You should now be able to see your new project with the modified configuration on the dashboard.
Editing and viewing existing projects
On the “My Projects” tab view, you can select a project and click the “View” button or click on the name of the project, and this will direct you to the project details page:
Next, click the "Edit & View Configuration" button to access the "Edit project" page. This page is identical to the "New project" page, except that your project information is already filled in.
On this page, you can edit and view the name and description of the project and view the configuration selected for the project. However, no changes related to the configuration are possible after project creation as all samples in a project need to be processed in the same manner. If a different configuration is required, a new project must be created.
You will be able to view additional details about the configuration in a grey box located in the top right corner of the page.
For older projects created before the inclusion of this information in a project configuration, you will be able to view the same basic details about the project but we cannot display any configuration details or modifications. In other words, you will not be able to see the grey box located in the top right corner of the page.
Once you’ve made your changes, you can click on the blue button "Save changes" to save your changes.
Now you should be taken back to the project details page, where you can see your changes have taken effect: