# Copy/Paste from https://data.broadinstitute.org/alkesgroup/Eagle/ Version 2.3.1 (March 3, 2017): Fixed bug causing rare crashes on samples with no hets. Fixed minor bugs in input reading. Improved error-checking and error-reporting. Version 2.3 (July 22, 2016): Added support for phasing chrX (and added chrX genetic map). Optimized performance when phasing sequence data without a reference. Disallowed REF/ALT swaps for indels even with --allowRefAltSwap. Improved error-checking. Version 2.2 (July 15, 2016): Added support for VCF/BCF input in non-reference mode. Reduced RAM when phasing sequence data in non-ref mode. Fixed bug causing crashes on samples with no hets. Fixed bug causing crashes on target hets monomorphic in the reference. Fixed other minor bugs. (Thanks to Stephan Ripke, Giulio Genovese, Christian Fuchsberger, and Sebastian Schoenherr for reporting bugs and assisting with debugging.) Version 2.1 (July 6, 2016): Replaced in-sample imputation algorithm; new algorithm fills in missing genotypes during phasing (improving overall efficiency on sequence data). Added experimental --usePS parameter for specifying FORMAT:PS phase set constraints (--usePS=1 for soft constraint; --usePS=2 for harder constraint). Fixed minor error in recombination probability formula. Fixed minor bug (incorrect memset call) in first step of non-reference-based phasing algorithm. Fixed bug in input-checking (incorrect exit upon finding ”.” genotypes in target VCF). Version 2.0.5 (May 26, 2016): Fixed bug in genetic map interpolation when using the --chrom flag. Version 2.0.4 (May 24, 2016): Added error check for 0 Mb / 0 cM region span; added error check for memory allocation failures. Version 2.0.3 (May 19, 2016): Added error check for 0 or 1 SNPs in intersection of target and ref. Version 2.0.2 (May 19, 2016): Added --allowRefAltSwap flag to allow swapping of REF/ALT in target vs. ref VCF. Version 2.0.1 (May 9, 2016): Fixed bug in region handling (thanks to Petr Danecek); added command line to VCF header. Version 2.0 (May 3, 2016): Initial release of Eagle2. Version 1.0 (September 23, 2015): Initial release of Eagle1.