Version 3.2.0

• Allow the optional definition of target_regions in the config for constraining variant calls (@johanneskoester, @kilpert).
• Update to latest freebayes and delly (@johanneskoester).

Version 3.1.0

• Update to Varlociraptor 4.6 (@johanneskoesrter)
• Merge closeby covered regions to improve freebayes parallelization (@christopher-schroeder)

Version 3.0.0

• This release updates to Varlociraptor 4.3, which requires a different specification of resolution in your scenario. You now need to specify the resolution as a step size, like 0.01. Basically this means: "how close do I want my estimated VAF to be to the true VAF". The smaller you choose this value, the more Varlociraptor has to compute. In other words, if you don't care too much about the actual VAF within an interval, you can set this to a value like 0.1. Otherwise, we suggest to keep the default, which is 0.01 (@johanneskoester, @tedil).
• Further, this release fixes several small bugs and caveats of the pipeline (@FelixMoelder, @johanneskoester ).

Version 2.0.6

• Fixed sample collection in vcf-report, thereby avoiding crashes on more complex scenarios.

Version 2.0.5

• Fixed an issue with Pandas on older machines by upgrading to Pandas 1.3.
• Unfortunately, this means that there can be another Pandas bug that causes an error in the render_scenario rule if the pandas version in your Snakemake environment is not also 1.3. This will be fixed with the release of Pandas 1.3.1 though, which should hopefully appear soon: https://github.com/pandas-dev/pandas/milestone/87.

Version 2.0.4

Use only a single thread for mosdepth, as it does not seem to scale beyond in our scenario.

Version 2.0.3

Min alternate freebayes count has to be 2 now, since 1 is anyway just leading to bias calls in Varlociraptor.

Version 2.0.2

Covered regions are now inferred using mosdepth instead of bedtools, leading to a speedup.

Version 2.0.1

• Freebayes and delly are now always limited to covered genome regions, in order to improve performance.

Version 2.0.0

• More flexible TMB configuration.
• Updated to Varlociraptor 4.1, which is able to detect additional artifacts in repeat regions and PCR homopolymer errors.