• Fixed bug in SKAT/SKATO tests when applying Firth/SPA correction
• Improved SPA implementation by computing both tail probabilities (previous implementation gave more conservative test with high case control imbalance)
• New option --set-singletons to specify which sites to include in singleton masks when building masks by adding a third column in the AAF file (see documentation)
• New option --l1-phenoList to run level 1 model only for a subset of the phenotypes when using --run-l1 (see wiki)
• Fixed bug in joint tests (occurred when some of the burden masks were ignored due to low MAC/failed test and program would crash)
• Fix bug when using apply-rint (introduced in v3.0.3)
• Added additional convergence criterion for ridge logistic regression based on fractional change
• Fix convergence issue for null Firth when fitted probabilities 0/1 occurred
• Fix format mismatch in sum stats file with joint tests (extra NA entry was added when input file had dosages)