- Update gatk4, tabix and rtg-tools
- Allow call caching of reference creation
- Switch to miniwdl for testing
- Add documentation for the pipeline.
- The pipeline output now contains summary tables for the SNPs and indels for
each sample, as well as an html report which plots the precision and
sensitivity for each sample (the data used is from
Threshold=None). - It is now possible to set a single baseline vcf file for all samples, using
fallbackBaselineVcf. - The default behaviour is now to ignore filtered variants
- Index for the baseline VCF file is now optional.