# Copy/Paste from https://data.broadinstitute.org/alkesgroup/BOLT-LMM/

Version 2.3.4 (August 10, 2019):
    Prevented environment variable MKL_NUM_THREADS from overriding --numThreads parameter.
Version 2.3.3 (August 3, 2019):
    Added support for missing values in BGEN v1.2 data.
    Reduced memory usage after completion of the model-fitting step (by freeing genotypes no longer needed during calculation of association tests for imputed variants).
    Updated BLAS library to Intel MKL 2019 Update 4 and modified bolt executable to dynamically link Intel threading library (libiomp5.so, now distributed with BOLT-LMM).
    Improved error-reporting and documentation; added FAQ section of this manual.
Version 2.3.2 (March 10, 2018):
    Added support for imputed X chromosome variants in the UK Biobank v3 imputation release (see section 9.1 for details).
    Added --bgenSampleFileList option to allow multiple bgen/sample file pairs with differing sample files.
    Changed the --allowX option to always be set (so --allowX is no longer needed for X chromosome analysis).
    Added --Nautosomes option for non-human analyses.
Version 2.3.1 (December 19, 2017):
    Added check for --covarFile when --covarCol or --qCovarCol are specified. (Previously, these arguments were silently ignored if --covarFile was not specified.)
    Added --allowX option for X chromosome analysis.
    Added section of documentation on analysis of case-control traits.
    Updated BLAS library to Intel MKL 2018 Update 1.
    Improved error-reporting and documentation.
Version 2.3 (August 1, 2017):
    Added multi-threaded support for BGEN v1.2 imputed file format used by UK Biobank.
    Added --bgenMinINFO parameter.
    Fixed P-value output for extremely small P-values previously rounded to zero.
    Fixed crash caused by very long BGEN allele names.
    Fixed bug in --noBgenIDcheck flag.
    Improved error-reporting.
    Added section at the end of this document providing recommendations for N=500K UK Biobank analyses.
Version 2.2 (Nov 13, 2015):
    Added support for testing imputed SNPs in BGEN format.
    Added option to look up LD scores by base pair coordinates rather than SNP name (--LDscoresMatchBp).
    Fixed bug in hg19 genetic map interpolation.
    Fixed bug in QC filter for per-sample missing rate.
    Improved error-checking.
Version 2.1 (Apr 29, 2015):
    Improved handling of IMPUTE2 files (large speedup; INFO output column instead of F_MISS; MAF filtering).
    Fixed bug in per-sample missingness filter (--maxMissingPerIndiv), which was being ignored.
    Implemented minor changes to input parameters (removed --impute2CallThresh, which had no effect; added --impute2MinMAF and --h2gGuess).
Version 2.0 (Mar 13, 2015):
    Added BOLT-REML algorithm for estimating heritability parameters. Fixed parameter-initialization bug that prevented BOLT-LMM from running on some systems. Implemented various minor improvements to parameter-checking.
    (Dec 8, 2014): Licensed source code under GPLv3.
Version 1.2 (Nov 4, 2014):
    Added support for testing imputed SNPs in 2-dosage format (Ricopili/plink2 format=2). Fixed bug causing nan heritability estimates.
Version 1.1 (Oct 17, 2014):
    Added support for testing imputed SNPs with probabilistic dosages.
Version 1.0 (Aug 8, 2014):
    Initial release.