Regenie v2.2

• Faster implementation of Step 1 and 2 (see here for details)
• New options --write-null-firth/--use-null-firth to store & re-use the estimates from approximate Firth null model
• New option --minCaseCount X to ignore binary traits with fewer than X cases (default is 10)
• New option --apply-rint to apply RINT to quantitative traits
• New option --write-mask-snplist to write the list of variants that went into each burden mask built on-the-fly in REGENIE
• Support of multiple files for options to filter variants/samples/sets [eg --extract]
• New option --starting-block to specify the block/set number at which to start Step 2
• New option --no-split to enforce output of summary stats to a single file for all traits
• New option --af-cc to output A1FREQ in case/controls separately in the step 2 result file
• Phenotypes analyzed in Step 2 with missing Step 1 predictions are now automatically ignored (unless using --ignore-pred)
• Samples with missing Step 1 predictions (i.e. PRS=NA) are automatically removed from Step 2 analysis
• New option --use-relative-path to use relative paths in the Step 1 output pred.list file instead of absolute paths
• Added support for tranposed phenotype file format with --tphenoFile

This version contains a bug for binary traits. Use version 2.2.1 instead

Regenie v2.0.2

• Bug fix for burden testing with BGEN files not in v1.2 with 8-bit encoding
• Enabled faster step 2 implementation with Zstd compressed BGEN files in v1.2 with 8-bit encoding

Regenie v2.0.1

• New option --catCovList to specify categorical covariates which will automatically be converted to dummy variables
• Enabled parameter expansion when specifying phenotypes/covariates to analyze [ e.g. --covarCol PC{1:10} ])

Regenie v2.0

• Added burden testing functionality for region or gene-based tests [see website for details]
• Added sample size column in summary stats output

Regenie v1.0.7

• Enabled for level 0 models in step 1 to be run in parallel [see Wiki page for details]

Regenie v1.0.6.9

• Improved step 2 for BGEN format files not in v1.2 and/or 8-bit encoding

Regenie v1.0.6.8

• New option --range to specify a chromosome region of variants to test in step 2

Regenie v1.0.6.7

• New option --print-prs in step 1 to print the whole genome predictions (i.e. PRS) without using LOCO;
• New flag --use-prs in step 2 to use these in the association testing step

Note: This version contains a bug when using --extract in step 2 with BGEN files not in v1.2 with 8-bit encoding. Use version 1.0.6.9 instead.

Regenie v1.0.6.6

Fixed MAC calculation for variants on sex chromosomes when sex information is available in the genotype file

All binaries are compiled with Boost Iostream library.

Regenie binary compiled with Intel MKL is regenie_v*_x86_64_Linux_mkl.zip

Regenie v1.0.6.5

Enabled options --extract/--exclude in step 2

All binaries are compiled with Boost Iostream library.

Regenie binary compiled with Intel MKL is regenie_v*_x86_64_Linux_mkl.zip