Version 3.6.2

Fix vcf-report

Version 3.6.1

Update VEP wrappers.

Version 3.6.0

• Update to Varlociraptor 4.11.

Version 3.5.0

• Allow handling of UMIs (@FelixMoelder)
• Fixed plots in vcf report (@FelixMoelder)
• Update to varlociraptor 4.10 (@johanneskoester)
• Update to rbt 0.38 (@johanneskoester)

Version 3.4.0

Update to Varlociraptor 4.9.

Version 3.3.0

• Update to Varlociraptor 4.7, including various model improvements that should overall lead to a much improved FDR control and more recognized artifacts, in particular on exome data with PCR amplification (@johanneskoester).
• Primer handling for amplicon sequencing with only a single primer per read pair (@FelixMoelder).

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.