Running SAIGE and SAIGE-GENE with the Glow Pipe Transformer is no longer supported. We recommend using GloWGR to perform association tests instead. For another example of the Glow Pipe Transformer, see Variant Annotation using Pipe Transformer.
GloWGR is a scalable whole genome regression method developed in collaboration with the Regeneron Genetics Center in open source with Project Glow. GloWGR is a distributed version of the single-node tool regenie (see the second version of the bioRxiv preprint). GloWGR is an enterprise-ready tool that provides equivalent accuracy to other methods for whole genome regression, but with an order-of-magnitude improvement in speed.
Run GloWGR in Databricks Runtime 7.0 for Genomics and above.
- The cluster configuration should use Databricks Runtime for Genomics.
- For best performance, use storage-optimized instances. We recommend i3.4xlarge.