Published January 9, 2021
| Version v1.2.5
Software
Open
bcbio/bcbio-nextgen: v1.2.5
Creators
- Brad Chapman1
- Rory Kirchner2
- Lorena Pantano2
- Sergey Naumenko
- Matthias De Smet3
- Luca Beltrame
- Tetiana Khotiainsteva
- Ilya Sytchev
- Roman Valls Guimera4
- John Kern
- Christian Brueffer5
- Vlad Savelyev6
- Guillermo Carrasco7
- Mario Giovacchini8
- Miika Ahdesmaki9
- Paul Tang10
- Sehrish Kanwal11
- James J Porter12
- Steffen Möller13
- Vang Le14
- Alexandru Coman15
- bogdang989
- Valentine Svensson16
- Brent Pedersen17
- Jeff Hammerbacher18
- Matt Edwards
- Meeta Mistry19
- apastore
- Peter Cock
- Stephen Turner20
- 1. Ginkgo Bioworks
- 2. Harvard Chan School of Public Health
- 3. @CenterForMedicalGeneticsGhent
- 4. University of Melbourne
- 5. Lund University Cancer Center
- 6. @populationgenomics
- 7. @iZettle
- 8. Science for Life Laboratory
- 9. AstraZeneca
- 10. startup
- 11. The University of Melbourne
- 12. Recurse Center
- 13. University of Rostock
- 14. Aalborg University
- 15. @tss-yonder
- 16. Serqet Therapeutics
- 17. University of Utah
- 18. @related-sciences
- 19. HSPH
- 20. University of Virginia
Description
1.2.5 (01 January 2021)
- Joint calling for RNA-seq variant calling requires setting
jointcallerto bring it in line with the configuration options for variant calling. - Allow pre-aligned BAMs and gVCFs for RNA-seq joint variant calling. Thanks to @WimSpree for the feature.
- Allow
CollectSequencingArtifactsto be turned off viatools_off: [collectsequencingartifacts]. - Fix getiterator -> iter deprecation in ElementTree. Thanks to @smoe.
- Add SummarizedExperiment object from RNA-seq runs, a simplified version of the bcbioRNASeq object.
- Add
umi_type: dragen. This enables bcbio to run with first-pass, pre-consensus called UMI BAM files from DRAGEN. - Turn off inferential replicate loading when creating the gene x sample RNA-seq count matrix. This allows loading of thousands of RNA-seq samples.
- Only make isoform to gene file from express if we have run express.
- Allow "no consensus peaks found" as a valid endpoint of a ChIP-seq analysis.
- Allow
BCBIO_TEST_DIRenvironment variable to control where tests end up. - Collect OxoG and other sequencing artifacts due to damage.
- Round tximport estimated counts.
- Turn off consensus peak calling for broad peaks. Thanks to @lbeltrame and @LMannarino for diagnosing the broad-peaks-run-forever bug.
Files
bcbio/bcbio-nextgen-v1.2.5.zip
Files
(17.8 MB)
| Name | Size | Download all |
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md5:9d4b004945f4ae4b36ae870e639939bc
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Additional details
Related works
- Is supplement to
- https://github.com/bcbio/bcbio-nextgen/tree/v1.2.5 (URL)