v1.0.1

Changes

• Fix bug when not skipping VQSR around publish dir

v1.0.0

Changes

Add support for RNAseq data

• When --skip_vqsr is passed then hard filters are applied to the HaplotypeCaller results. default values for the thresholds are the recommended in (Brouard & Bissonnette, 2022). These defaults can be changed with --indels_hard_filters and --snvs_hard_filters
• A minimum Phred confidence can be now passed to the HaplotypeCaller. The recommendation for RNA is 20, the default is to apply no filter.
• In contradiction with GATK defaults and best practices we are explicitly excluding soft clipped bases. This behaviour can be changed using --use_soft_clipped_reads

Release v0.3.0

Changes

• Add parameters --input_bam and --input_name for an individual sample

Release v0.2.0

Changes

• Add option to skip the Variant Quality Score Recalibration (--skip_vqsr). This comes handy for non human organisms where all required resources are not available
• Support for replicates. Multiple BAM files can be provided for the same sample in the input table
• Support for non diploid organisms through --ploidy parameter
• Add some more tests

Release v0.1.4

Bugfix

Provide VCF index to VQSR process

Release v0.1.3

Bugifx

Fix issue with --truth-sensitivity-filter-level parameeter in ApplyVQSR

Release v0.1.2

Fix issue with --truth-sensitivity-filter-level

Release v0.1.1

First tentative version implementing the HaplotypeCaller best practices.