Published March 17, 2020
| Version v3.0.0
Software
Open
biowdl/RNA-seq: Release 3.0.0
- 1. @LUMC
- 2. Leiden University Medical Center
- 3. LUMC
Description
In version 3.0.0 the RNA-seq pipeline was brought up to date with the GATK best practices pipeline. Several errors in the variant calling part of the pipeline were fixed.
- UMI deduplication stats collection is now optional.
- Add scatterSize option to centrally control the scatter size
- Multisample VCFs are no longer generated for RNA-seq by default as this is not GATK best practice. It can optionally be turned on again.
- Add proper copyright headers to WDL files. So the free software license is clear to end users who wish to adapt and modify.
- Added UMI based deduplication as an optional step.
- Major fix: Joint genotyping is not performed on RNA-seq reads. Instead, each sample is genotyped seperately by the HaplotypeCaller.
- Major fix: base recalibration is now applied after splitting the cigar reads. previously this was done in an erroneous manner.
- Structs are removed from the input.
- Fixed a typo in the inputs: detectNovelTranscipts -> detectNovelTranscripts.
- Removed a number of unused inputs ("dbsnp", "targetIntervals", "ampliconIntervals" and "variantCalling") from the sample workflow.
- Added input overview to docs.
- Added WDL-AID to linting.
- Update default htseq image version to 0.11.2
Files
biowdl/RNA-seq-v3.0.0.zip
Files
(4.8 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/biowdl/RNA-seq/tree/v3.0.0 (URL)