- Faster implementation of Step 1 and 2 (see here for details)
- New options
--write-null-firth/--use-null-firthto store & re-use the estimates from approximate Firth null model - New option
--minCaseCount Xto ignore binary traits with fewer than X cases (default is 10) - New option
--apply-rintto apply RINT to quantitative traits - New option
--write-mask-snplistto write the list of variants that went into each burden mask built on-the-fly in REGENIE - Support of multiple files for options to filter variants/samples/sets [eg
--extract] - New option
--starting-blockto specify the block/set number at which to start Step 2 - New option
--no-splitto enforce output of summary stats to a single file for all traits - New option
--af-ccto output A1FREQ in case/controls separately in the step 2 result file - Phenotypes analyzed in Step 2 with missing Step 1 predictions are now automatically ignored (unless using
--ignore-pred) - Samples with missing Step 1 predictions (i.e. PRS=NA) are automatically removed from Step 2 analysis
- New option
--use-relative-pathto use relative paths in the Step 1 output pred.list file instead of absolute paths - Added support for tranposed phenotype file format with
--tphenoFile
This version contains a bug for binary traits. Use version 2.2.1 instead