Getting the variants out is where the analysis starts. What does the variation mean, which ones correlate with a detectable phenotype. Which ones are affecting

Getting the variants out is where the analysis starts. What does the variation mean, which ones correlate with a detectable phenotype. Which ones are affecting regulatory systems. Genomics England is brilliant because it has good access to excellent NHS data which it will use to do a lot of analysis. Which its not getting off the shelf but a lot of talented clincal+bio+informaticians are working hard on that. Or in other words getting the variants to the human genome reference is just the start of the analysis not the end. i.e. I am more worried about the end of the pipeline than the contents of them. I suspected as much on the 1,2,3 level. But even 2 is not really fixed yet. There are great off the shelf tools but even the concept of variation calling against a reference linear genome is not perfect yet especially with the alt_loci business. Which driving the variation graph work in the GA4GH projects.