regenie is a C++ program for whole genome regression modelling
of large genome-wide association studies. It is developed and supported by a team of scientists at the Regeneron Genetics Center. regenie employs the BGEN library.

References:

• Joelle Mbatchou, Leland Barnard, Joshua Backman, Anthony Marcketta, Jack A. Kosmicki, Andrey Ziyatdinov, Christian Benner, Colm O'Dushlaine, Mathew Barber, Boris Boutkov, Lukas Habegger, Manuel Ferreira, Aris Baras, Jeffrey Reid, Goncalo Abecasis, Evan Maxwell, Jonathan Marchini.
  Computationally efficient whole genome regression for quantitative and binary traits
  bioRxiv (2020),doi: https://doi.org/10.1101/2020.06.19.162354.
  
• Band, G. and Marchini, J.
  BGEN: a binary file format for imputed genotype and haplotype data
  bioRxiv (2018); doi: https://doi.org/10.1101/308296

• regenie Github page
• regenie_Tutorial
• BGEN home page

• Module Name: regenie (see the modules page for more information)
• Unusual environment variables set
  • REGENIE_HOME  installation directory
  • REGENIE_BIN       executable directory
  • REGENIE_SRC       source code directory
  • REGENIE_DATA  sample data and checkpoints directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn3101 ~]$module load regenie/3.0.3  
[+] Loading singularity  3.10.0  on cn3063
[+] Loading regenie  3.0.3

[user@cn3101]$ ls $REGENIE_BIN 
bgenix  cat-bgen  edit-bgen  regenie  zstd

[user@cn3101]$ regenie --help
              |============================|
              |        REGENIE v3.0.3      |
              |============================|

Copyright (c) 2020-2022 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.


Usage:
  /regenie/regenie [OPTION...]

  -h, --help      print list of available options
      --helpFull  print list of all available options

 Main options:
      --step INT                specify if fitting null model (=1) or
                                association testing (=2)
      --bed PREFIX              prefix to PLINK .bed/.bim/.fam files
      --pgen PREFIX             prefix to PLINK2 .pgen/.pvar/.psam files
      --bgen FILE               BGEN file
      --sample FILE             sample file corresponding to BGEN file
      --ref-first               use the first allele as the reference for
...

[user@cn3101]$ cp $REGENIE_DATA/* .

[user@cn3101]$ regenie --bgen example.bgen --out my_output --step 1 --bsize 200 --phenoFile phenotype_bin.txt
Start time: Tue Aug 16 13:24:00 2022

              |============================|
              |        REGENIE v3.0.3      |
              |============================|

Copyright (c) 2020-2022 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini.
Distributed under the MIT License.

Log of output saved in file : my_output.log

Options in effect:
  --bgen example.bgen \
  --out my_output \
  --step 1 \
  --bsize 200 \
  --phenoFile phenotype_bin.txt

Fitting null model
 * bgen             : [example.bgen]
   -summary : bgen file (v1.2 layout, zlib compressed) with 500 named samples and 1000 variants with 8-bit encoding.
   -index bgi file [example.bgen.bgi]
 * phenotypes       : [phenotype_bin.txt] n_pheno = 2
   -keeping and mean-imputing missing observations (done for each trait)
   -number of phenotyped individuals  = 500
 * number of individuals used in analysis = 500
   -residualizing and scaling phenotypes...done (0ms)
 * # threads        : [55]
 * block size       : [200]
 * # blocks         : [5] for 1000 variants
 * # CV folds       : [5]
 * ridge data_l0    : [5 : 0.01 0.25 0.5 0.75 0.99 ]
 * ridge data_l1    : [5 : 0.01 0.25 0.5 0.75 0.99 ]
 * approximate memory usage : 2MB
 * setting memory...done

Chromosome 1
 block [1] : 200 snps  (4ms)
   -residualizing and scaling genotypes...done (3ms)
   -calc working matrices...done (420ms)
   -calc level 0 ridge...done (79ms)
 block [2] : 200 snps  (2ms)
   -residualizing and scaling genotypes...done (1ms)
   -calc working matrices...done (439ms)
   -calc level 0 ridge...done (79ms)
 block [3] : 200 snps  (2ms)
   -residualizing and scaling genotypes...done (1ms)
   -calc working matrices...done (483ms)
   -calc level 0 ridge...done (81ms)
 block [4] : 200 snps  (3ms)
   -residualizing and scaling genotypes...done (1ms)
   -calc working matrices...done (366ms)
   -calc level 0 ridge...done (78ms)
 block [5] : 200 snps  (2ms)
   -residualizing and scaling genotypes...done (1ms)
   -calc working matrices...done (485ms)
   -calc level 0 ridge...done (78ms)

 Level 1 ridge...
   -on phenotype 1 (Y1)...done (0ms)
   -on phenotype 2 (Y2)...done (0ms)

Output
------
phenotype 1 (Y1) :
  0.01  : Rsq = 0.00292408, MSE = 0.995083<- min value
  0.25  : Rsq = 0.00619743, MSE = 0.998022
  0.5   : Rsq = 0.00679147, MSE = 1.00153
  0.75  : Rsq = 0.00753375, MSE = 1.00367
  0.99  : Rsq = 0.00733694, MSE = 1.01373
  * making predictions...writing LOCO predictions...done (9ms)

phenotype 2 (Y2) :
  0.01  : Rsq = 0.012437, MSE = 0.98745<- min value
  0.25  : Rsq = 0.00739346, MSE = 0.997094
  0.5   : Rsq = 0.00612812, MSE = 1.00169
  0.75  : Rsq = 0.00621549, MSE = 1.00343
  0.99  : Rsq = 0.0082828, MSE = 1.00621
  * making predictions...writing LOCO predictions...done (9ms)

List of blup files written to: [my_output_pred.list]

Elapsed time : 2.66076s
End time: Tue Aug 16 13:24:02 2022

[user@cn3101 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$