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Changes in Beagle 5.0
=========================
* Much faster genotype phasing and genotype imputation algorithms.
* An improved reference file format: bref3 which supersedes bref version 2.
* Window and overlap parameters use centiMorgan units.
* Some user parameters are changed (see documentation).
* Refined IBD algorithm removed from Beagle and made a stand-alone program.
* Input VCF file must contain genotype (GT) fields (GL/PL fields are ignored).
Beagle 5.0 (14May18.ff7) release notes
=============================================
* First release of Beagle version 5.0
Beagle 5.0 (16May18.771) release notes
=============================================
* Fixed a bug when phasing and imputing in the same analysis
Beagle 5.0 (24May18.276.jar) release notes
=============================================
* Minor modification to phasing algorithm
Beagle 5.0 (28May18.405) release notes
=============================================
* Fixed a concurrency bug
Beagle 5.0 (30May18.3bb) release notes
=============================================
* Improved error messages
Beagle 5.0 (04Jun18.a80) release notes
=============================================
* Fixed a bug in phasing when ALT field is '.'
Beagle 5.0 (10Jun18.811) release notes
=============================================
* Fix bug appearing when there is a large inter-marker distance
Beagle 5.0 (03Jul18.40b) release notes
=============================================
* Fixed a bug appearing when reference panel ALT field is '.'
Beagle 5.0 (10Sep18.879) release notes
=============================================
* Fixed a bug in imputation output when reference panel ALT field is '.'
Beagle 5.0 (15Sep18.8a0) release notes
=============================================
* Fixed a bug appearing when analysis window has only one target marker
Beagle 5.0 (28Sep18.793) release notes
=============================================
* Refactored some classes
Beagle 5.0 (16May19.351) release notes
=============================================
* Refactored some classes
* Fixed a concurrency bug
Beagle 5.0 (03Jul19.b33) release notes
=============================================
* Fixed a bug when analysis includes multiple chromosomes
Beagle 5.0 (12Jul19.0df) release notes
=============================================
* Improved an error message
* Improved handling of inconsistent marker order in ref and gt files
Beagle 5.1 (13Aug19.a31) release notes
============================================
* Initial release of Beagle 5.1
* Beagle 5.1 has some improvements that increase speed and accuracy
Beagle 5.1 (24Aug19.3e8) release notes
============================================
* Fixed a bug that can arise when phasing inbred samples
Beagle 5.1 (21Sep19.ec3) release notes
============================================
* Fixed bugs when phasing or imputing using a reference panel
Beagle 5.1 (08Nov19.3ec) release notes
============================================
* Add support for male, haploid chrom X genotypes
Beagle 5.1 (20Nov19.573) release notes
============================================
* Fixed bug when number of marker alleles is >= number of samples
Beagle 5.1 (25Nov19.28d) release notes
============================================
* Increased robustness to genetic maps with small inter-marker distances
Beagle 5.1 (13Mar20.38e) release notes
============================================
* Improve robustness to rounding error
* Fix a concurrency bug
Beagle 5.1 (21Mar20.d65) release notes
============================================
* Fix a bug in reference-based phasing
Beagle 5.1 (24Mar20.5f5) release notes
============================================
* Improve robustness when some samples have high rates of missing genotypes
Beagle 5.1 (27Apr20.b81) release notes
============================================
* Improve robustness when many markers have high rates of missing genotypes
Beagle 5.1 (18May20.d20) release notes
============================================
* Fix a concurrency bug
Beagle 5.1 (18May20.d20) release notes
============================================
* Fix a concurrency bug
Beagle 5.2 (05Apr21.9b7) release notes
============================================
* Initial release of Beagle 5.2
* Version 5.2 provides significantly faster genotype phasing than version 5.1
Beagle 5.2 (17Apr21.dc6) release notes
============================================
* Increase robustness when phasing unusual data sets
Beagle 5.2 (21Apr21.304) release notes
============================================
* Fix bug causing small loss in accuracy when phasing sequence data
Beagle 5.2 (29May21.d6d) release notes
============================================
* Increase robustness to high rate of missing genotypes
Beagle 5.2 (28Jun21.220) release notes
============================================
* Improve robustness when many markers have a high rate of missing genotypes
Beagle 5.3 (08Feb22.fa4) release notes
============================================
* Initial release of Beagle 5.3
* Version 5.3 has improved parameter estimation when analyzing non-human data
* Version 5.3 has an "em" parameter that can turn off parameter estimation.
Beagle 5.4 (19Mar22.0da) release notes
============================================
* Initial release of Beagle 5.4
* Version 5.4 is more robust to poorly-estimated genetic maps
* Version 5.4 has modestly lower memory requirements
Beagle 5.4 (25Mar22.4f6) release notes
============================================
* Fix a logic bug.
Beagle 5.4 (12Apr22.32e) release notes
============================================
* Allow break-end replacement strings in ALT alleles
Beagle 5.4 (18Apr22.4de) release notes
============================================
* Improve error messages
* Reduce memory use
Beagle 5.4 (19Apr22.7c0) release notes
============================================
* Fix a bug that can be triggered when the ALT field is "."
Beagle 5.4 (05May22.33a) release notes
============================================
* Fix an output-truncating bug when combining ref and chrom parameters
Beagle 5.4 (22Jul22.46e) release notes
============================================
* Fix a bug in calculating the cumulative marker count
Beagle 5.4 (01Mar24.d36) release notes
============================================
* Add an output VCF meta-information line for the INFO/END field
Beagle 5.4 (27May24.118) release notes
============================================
* Fix a file decompression bug
Beagle 5.4 (06Aug24.a91) release notes
============================================
* Restore Java 8 compatibility
Beagle 5.4 (29Oct24.c8e) release notes
============================================
* Improve handling of atypical input data
Beagle 5.5 (beagle.17Dec24.224.jar) release notes
============================================
* Initial release of Beagle 5.5
* Add window-markers parameter to control maximum markers per window
Beagle 5.5 (27Feb25.75f) release notes
============================================
* Fix a bug that could cause a run-time exception
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