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All notable changes to this project are documented in this file.

Version 5.1.1 is now available [here] ( as docker image or static binaries.


* Bugfix of a nasty segfault, thanks to Ami Williams (23andMe).
* Correctin of a mistake in Ligate documentation   
* Bugfixes when reading multiple input files data	


* Second release / Version used for phasing UKB WGS 200k data
* Chromosome X support added in phase_[common/rare]
* Pedigree phasing support added in phase_[common/rare/ligate]
* Many small optimizations in phase_[common/rare]
* IBD2 protection improved in phase_common abd added in phase_rare
* Automatic indexing of VCF/BCF files	


* First release / Version used for the preprint. (

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Copyright © 2022-2023 Olivier Delaneau | All Rights Reserved | SHAPEIT5 executables and source code are distributed under the MIT license.