Regenie v3.2.6

• Relax tolerance parameter for null unpenalized logistic regression from 1e-8 to 1e-6
• Bug fix for SKATO when one of the p-values at fixed rho was numerically 0
• More verbose debugging messages

Regenie v3.2.5.3

• Fix inflation issue when testing main effect of SNP in GxE model (due to rare variants tested with robust SE)
• Bug fix for issue #393

Regenie v3.2.5

• Use ACAT to get SBAT p-value across POS/NEG models
• Use pseudo-data representation algorithm as default in step 2 single variant Firth tests (Newton-Raphson algorithm is used as fallback if former fails) to address Firth convergence issues
• Bug fix for ACATV when set has a single variant with zero weight

Regenie v3.2.4

• Relaxed the requirement on the minimum number of unique values for QTs to 3 from 10
• Fix bug in joint tests on burden masks which caused the software to crash
• Fix bug which occurred in ACATV when mask contained a single variant and its p-value was NA

Regenie v3.2.3

• Address convergence issues for Firth regression by using pseudo-data representation based on the brglm R package
• Allow for gzipped pvar/psam/bim/fam files (ie file name ending in .gz)
• Reduce computation time for conditional analyses when a large number of conditional variants are present
• Bug fix for sumstats formatting in multi-trait runs with --no-split and joint tests
• Bug fix for SBAT when P>N

Regenie v3.2.2

• Add new columns in sumstats file (N_CASES/N_CONTROLS) to output the number of cases/controls when using --af-cc (#348)
• Bug fix for LOVO with ultra-rare variants in SKAT/ACAT tests
• Bug fix for SKATO with negative variance (#342)
• Bug fix when chisq test statistic is numerically <0
• Bug fix to allow to skip association testing (--skip-test) when only writing out the list of variants in each mask (--write-mask-snplist)
• Bug fix to correctly catch phenotype failing either null logistic regression or null logistic Firth in step 2 and write the phenotype names to file
• Reduce convergence issues with logistic regression null model

Regenie v3.2.1

• Improve efficiency of LOVO scheme for large sets to significantly reduce memory usage
• New option --lovo-snplist to only analyze subset of the LOVO masks when running the LOVO scheme
• Bug fix for SPA due to numerical overflow when using exp()
• For SKAT/ACAT tests with Firth correction, SKAT weights are now excluded when applying Firth test on the single variants (leads to better numerical stability for the ultra-rare variant masks in the presence of high imbalance)

Regenie v3.2

• Bug fix for SKAT/SKATO when testing on binary traits using Firth/SPA (introduced in v3.1.1)
• Switched name of NNLS joint test to SBAT altering the name of corresponding options:
  • --joint sbat instead of --joint nnls
• Bonferroni correction is now applied before reporting the SBAT test p-value [to correct for taking minP of 2 tests]
• Added warning for heterozygous males in chrX non-PAR regions (males should be coded as diploid [0/2] for chrX) - hard-call mode only

Regenie v3.1.4

• New option --par-region to specify build to determine bounds for chrX PAR regions
• New option --force-qt to force QT runs for traits with fewer than 10 values [otherwise will throw an error]
• Phenotype imputation for missing values is now applied after RINTing when using --apply-rint (instead of before)
• Bug fix to catch when number of covariates is greater than sample size
• Bug fix in SKAT/ACAT tests when set consisted only of ultra-rare variants & would be skipped
• Bug fix for overflow error when running SKATO

Regenie v3.1.3

• Bug fixes to address Firth convergence issues and error when using with --catCovarList with --interaction