We recommend using GloWGR to perform association tests. To distribute other bioinformatics tools such as SAIGE, use 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 provides equivalent accuracy to other methods for whole genome regression, but with an order-of-magnitude improvement in speed.
- For best performance, use storage-optimized instances. We recommend i3.4xlarge.