• Timing reduction for single variant association tests in step 2 with hard-call genotype data (e.g. WES/WGS).

• New option --weights-col to specify custom weights to use in gene-based tests (see doc for details)
• New option --htp to output summary statistics in the HTP format which is used by the remeta software
  • By default, p-values are capped at 2.2E-307. To avoid this, use --exact-p.
• New option --skip-dosage-comp to skip dosage compensation for males in non-PAR chrX regions
  • By default, REGENIE assumes males are coded as 0/2 in the non-PAR regions of the genotype file
  • With this option, male genotypes (or dosages) will be divided by 2 in non-PAR regions (i.e. male genotypes will be on a [0,1] scale while females will be on a [0-2] scale)
• Bug fix to skip non-burden tests when running GxE or GxG interaction tests
• Bug fix for #579
• Address convergence issue when fitting null model with Firth
• Relax threshold used to check variance of tested SNPs after removing covariate effects
• Check that none of the covariates are also specified as phenotypes (in which case they will be excluded from the covariate list)