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Regenie v4.1

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@joellembatchou joellembatchou released this 27 Jan 21:24
· 23 commits to master since this release
v4.1
4b67616
  • Timing reduction for single variant association tests in step 2 with hard-call genotype data (e.g. WES/WGS).
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  • 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)
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