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.

Version 1.5.0

• Added linkouts to VarSEAK (@FelixMoelder).
• Updated to newer tool versions in case of GATK base recalibration (should fix issues with system setting for temp files not being used) and varlociraptor (should get rid of some SNV and MNV artifacts) (@johanneskoester).

Version 1.4.0

• Auto-detect insert size when mapping primer sequences (@dlaehnemann).
• Improved schemas for config and sample sheets (@johanneskoester).

Version 1.3.2

• Fixed a bug with delly calls inducing an invalid BCF when being annotated.

Version 1.3.1

Attention, this version introduces changes in the config file:

• Allow to filter by local FDR instead of global FDR (example).
• Generalized custom parameter settings for varlociraptor config (example).

Version 1.3.0

• Update to Varlociraptor 3.4.0.

Version 1.2.0

• allow commenting lines in sample and unit sheets (@tedil)
• improved documentation (@johanneskoester)
• bump htslib versions (@tedil)

Version 1.1.0

• Upgrade to Varlociraptor 3.1 (@johanneskoester)
• Best-practice formatting (@johanneskoester)
• Fixed reporting rules (@dlaehnemann, @jafors)