rgcgithub/regenie: Regenie v4.1

Timing reduction for single variant association tests in step 2 with hard-call genotype data (e.g. WES/WGS). <img width="490" alt="image" src="https://github.com/user-attachments/assets/52bccb2c-24bc-490a-b306-11737d9e6b67" />

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)