SAVANA 1.2.4

Implements a minor bugfix when calling savana run as raised in #50

SAVANA 1.2.3

• New approach for allele-counting, improving speed and performance
• Improved copy number output
• Added additional copy number parameters
• Improved documentation for copy number
• Added --overwrite flag to force continue even if files present in outdir
• Coverage bins bugfix

SAVANA 1.2.2

Minor updates:

• Adding separate --cna_threads argument
• Minor README updates
• Bugfix for cna rescue
• Bugfix for custom classification JSON example
• Subset bam example

SAVANA 1.2.1

SAVANA 1.2.1 - Minor fixes:

• parameter fix to make cn_binsize optional (default = 10kbp)
• allow savana cna use without blacklist
• fix for when reference fasta is not sorted to extract canonical contigs for cna analysis

SAVANA 1.2.0

SAVANA 1.2.0 - Major Release:

• copy number aberration (CNA) calling
• phasing information from input bams used
• additional fields in the VCF

various algorithm improvements

Version 1.0.5

Bugfix for model failing to classify when an SV type was not present (#37)

Version 1.0.4

• Removing the 'beta' in the version printed during runtime.

This version should resolve the conda/mamba install errors raised in #27

Version 1.0.3

• Add CRAM support (with caveats)
• Fix bug with model classification
• Adding missed dependencies for model training
• Narrowing allowable random forest search for model training

V1 of SAVANA

Major Release.

• Adds functionality to use a machine-learning classifier to categorise variants (in addition to custom filtering and support for legacy methods)
• Adds read depth to VCF
• Sorts output VCF files
• Includes savana command in VCF output

In addition to many more changes. Please refer to the updated README for a full explanation of how to use SAVANA v1.

0.2.3-beta

• Label VCF output file with a custom/inferred sample name
• Adding MATEID and SVTYPE fields to VCF (SVTYPE=BND for all except INS)