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:
- 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 imputed haplotypes.
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.