0.3-alpha

This is a major release that contains significant new features and improvements.

New features

• Variant filtering: Octopus now has simple threshold based filtering which is turned on by default. This can dramatically reduce the false positive rate in some datasets (e.g. Platinum genomes).
• The population model now uses an independence-based genotype model. Although this doesn't offer true joint calling, it at-least offers consistent output until such time as a proper model is implemented.
• Somatic mutation calling is now significantly faster and more accurate due to model optimisation.

Bug fixes

• Fixed a bug with haplotype filtering that could cause haplotypes not to be filtered, and also result in inconsistent results between runs.

Other changes

• VCF records now include AC and AN INFO fields.
• Added an official logo!
• Protect called haplotypes from filtering when using holdouts.
• Octopus will now always emit a call if the variant posterior is above the given threshold, even if the homozygous reference genotype is MAP.
• The max QUAL is now 10000.