Issues

• Step2 convergence of t2e analysis with tied events

  rgcgithub/regenie#697 · Filter by author paulbeele2 opened on Sep 11, 2026
  1

• guidance on applying GENE_P tests to multiple datasets

  rgcgithub/regenie#693 · Filter by author evanslm opened on Aug 27, 2026
  2

• Guidance on --t2e-l1-pi6 for low-heritability T2E trait — Level 1 model fails to converge without it

  rgcgithub/regenie#691 · Filter by author RamonaZwamborn opened on Aug 14, 2026
  1

• Inflation of beta-values from logistic analysis - it is version specific

  rgcgithub/regenie#684 · Filter by author nievergeltlab opened on Mar 2, 2026
  2

• Ordinal/categorial traits

  enhancement
  rgcgithub/regenie#681 · Filter by author JordanBoulais opened on Feb 13, 2026
  1

• Support vcf/bcf format for structural variants

  enhancement
  rgcgithub/regenie#677 · Filter by author jjfarrell opened on Jan 9, 2026

• Conditional analysis with multiple variants

  rgcgithub/regenie#676 · Filter by author Nobuyuki-Enzan opened on Dec 31, 2025
  1

• Guidance for Gene-level test Gene_P

  rgcgithub/regenie#675 · Filter by author zyh4482 opened on Dec 22, 2025
  1

• how to define minMAC for generic burden test?

  rgcgithub/regenie#674 · Filter by author sinhanushka12 opened on Dec 15, 2025
  1

• Feature request: Allow writing masks to plink2 (pgen) file format so that non-integer weighted genotypes can be captured

  rgcgithub/regenie#671 · Filter by author dvg-p4 opened on Nov 6, 2025

• P-values not calculated in interaction testing

  rgcgithub/regenie#669 · Filter by author IchigoJiken opened on Oct 21, 2025

• Regenie requires FID to be present in .psam files although it is optional in the spec

  rgcgithub/regenie#666 · Filter by author pettyalex opened on Sep 28, 2025
  1

• Feature request: Support providing both domain and weights at the same time

  enhancement
  rgcgithub/regenie#655 · Filter by author dvg-p4 opened on Aug 18, 2025

• conda installation stuck on "solving environment"

  rgcgithub/regenie#652 · Filter by author fciamponi opened on Jul 14, 2025

• Inquiry on "Level 1 model did not converge" in step1

  rgcgithub/regenie#648 · Filter by author WZo0o opened on Jul 4, 2025

• Speed issues - MKL library + Boost Iostream vs None

  rgcgithub/regenie#645 · Filter by author Tahai-nformatics opened on Jun 24, 2025
  1

• Some issues during the step1 process

  rgcgithub/regenie#644 · Filter by author JhGoodLuck opened on Jun 21, 2025
  1

• Gene-based test inconsistencies

  rgcgithub/regenie#643 · Filter by author sbguarch opened on Jun 13, 2025
  1

• Gene modifier analysis in Regenie

  rgcgithub/regenie#638 · Filter by author ggstatgen opened on May 30, 2025

• Cox regression with Firth correction did not converge

  rgcgithub/regenie#635 · Filter by author Susie528 opened on May 23, 2025

• Questions on Using Region-Based SNPs and Multiple Phenotypes in REGENIE for PheWAS

  rgcgithub/regenie#632 · Filter by author HYEONJIN21 opened on May 15, 2025
  2

• step2.1, inflated p-values - what could be the issue?

  rgcgithub/regenie#631 · Filter by author zx8754 opened on May 13, 2025
  1

• Potential Issue with Gene-set or Pathway based burden analysis

  rgcgithub/regenie#630 · Filter by author BarisKayaalp opened on May 13, 2025
  1

• Question Regarding the a1freq_controls

  rgcgithub/regenie#629 · Filter by author xyy1093 opened on May 12, 2025
  13

• Regenie Step 1, all predictions are nan

  rgcgithub/regenie#627 · Filter by author DelnazRoshandel opened on May 2, 2025
  8