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v1.9

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@edg1983 edg1983 released this 26 Oct 11:14
· 24 commits to main since this release
v1.9
efdaebb

This is a massive new release including many new features:

  • analysis is now fully parallelized in step 1 for both L0 and L1 levels. This reduces the resources requested for L1 regression and speeds up analysis, especially when analyzing a large batch of binary phenotypes
  • the pipeline can now accept for step 2 a dataset provided in multiple chunk files (convenient for large WGS cohorts where data may be provided as multiple chunk files)
  • new multi-projects mode that allows you to provide a manifest file describing multiple projects to be run together. This provides a convenient way to configure similar analyses when you have pre-processed phenotype/covariate data. For example, you want to test various combinations of covariates for the same phenotypes, or you want to replicate the same analysis using different conditional snp lists or GxE / GxG variables.
  • VCF input dataset is now converted to bgen instead of pgen to improve perfomances
  • drop the need for a snplist file to split step2 execution when you use BGEN input. This simplifies the input and avoids unnecessary additional step for snplist generation.
  • you can now perform GxE and GxG analysis at step2 by providing a covariate or a variant ID to test interaction
  • you can perform conditional analysis in step2 providing a list of SNP to condition on
  • analysis can now be restricted to a specific variant list and/or gene list (not compatible with step2 split analysis)
  • improved reports rendering for long tables of top hits / top loci
  • various bug fixes
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