Regenie v1.0.6.4

• New option --minINFO to filter imputed variants in Step 2 by the imputation info score
• Edited Makefile to compile with Intel MKL if installed

All binaries are compiled with Boost Iostream library.

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

Regenie v1.0.6.3

Improved ridge logistic regression to avoid convergence issues in step 1 with low case-count traits

All binaries are compiled with Boost Iostream library.

Regenie v1.0.6.2

New option --ref-first to use the first allele for each variant as the reference allele for BGEN or PLINK bed/bim/fam file input [default is to use the last allele as the reference]

v1.0.6.2.gz corresponds to binaries compiled with Boost Iostream library.

Regenie v1.0.6.0

• Improve logistic regression implementation to address convergence issues with low case counts
• Add new option --firth-se to compute SE using effect size estimate and LRT p-value when using Firth correction (rather than from Hessian for the unpenalized log-likelihood)

v1.0.6.0.gz corresponds to binaries compiled with Boost Iostream library

Regenie v1.0.5.9

Fixed bug printing variant ID when variant with variance = 0 occurs in step 1

v1.0.5.9.gz corresponds to binaries compiled with Boost Iostream library

Regenie v1.0.5.8

Fixed bug due to input genotype file not sorted by chromosome and one of options --extract/--exclude/--chr/--chrList is used.

v1.0.5.8.gz corresponds to binaries compiled with Boost Iostream library

Regenie v1.0.5.7

New option --with-bgi to read variant information from a .bgi index file for BGEN input format
New option --write-samples to write IDs of samples analyzed for each trait in step 2
Added Mach Rsq information score for PGEN input format in step 2

v1.0.5.7.gz corresponds to binaries compiled with Boost Iostream library

Regenie v1.0.5.6

+Enabled output of LOCO predictions files (step 1) and association result files (step 2) in gzip compressed format using option --gz [it requires compiling with Boost Iostream library (see Install tab of the webpage)]
+Added automatic removal from the analysis of genotyped samples in step 2 not present in the LOCO prediction files from step 1 [done separately for each trait]

v1.0.5.6.gz corresponds to binaries compiled with Boost Iostream library

Regenie v1.0.5.5

+Fixed bug when setting the total number of blocks [the bug was introduced in v1.0.5.3]
+Addressed bug in step 1 with boost filesystem on some machines due to invalid LC_ALL locale