- Both union and intersection from each SV types are generated.
- The pipeline now first seperate SVs by types before merging.
- Duphold can now be run optionally to annotate and remove FP deletions and duplications.
- Replace excludeFpDupDel-option with runDuphold-option: DupHold annotation and FP filtering are now optional together.
- Update CLEVER dockerimage.
- DELLY: Update docker image.
- Structural-variantcalling pipeline: Remove GRIDSS from the pipeline.
- Exclude GRIDSS from SURVIVOR merging: SVs were only defined as BNDs in GRIDSS.
- Optional filtering of missing and hom-ref genotypes.
- Optional filtering of FP deletions and duplications.
- Add DUPHOLD: annotate SVs with depth values.
- Make bcftools indexing optional.
- Structural-variantcalling pipeline: add sorting and change id.
- Added GRIDSS sv caller
- Bcftools samtools and picard images are updated to newer versions.
- Bcftools view now converts delly vcf to a gzipped version.
- Tasks were updated to contain the
time_minutes
runtime attribute and associatedtimeMinutes
input, describing the maximum time the task will take to run.
- Add WDL task for smoove SV-caller.
- Created a structural variant-calling pipeline.