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Published September 21, 2020 | Version v1.2.4
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bcbio/bcbio-nextgen: v1.2.4

Authors/Creators

  • 1. Ginkgo Bioworks
  • 2. Harvard Chan School of Public Health
  • 3. @CenterForMedicalGeneticsGhent
  • 4. @UMCCR
  • 5. University of Melbourne
  • 6. Lund University Cancer Center
  • 7. @iZettle
  • 8. Science for Life Laboratory
  • 9. AstraZeneca
  • 10. startup
  • 11. The University of Melbourne
  • 12. Recurse Center
  • 13. Aalborg University
  • 14. University of Rostock
  • 15. @tss-yonder
  • 16. FL60 Inc
  • 17. University of Utah
  • 18. @related-sciences
  • 19. HSPH
  • 20. University of Virginia

Description

1.2.4 (21 September 2020)
  • Remove deprecated --genomicsdb-use-vcf-codec option as this is now the default.
  • Add bismark output to MultiQC.
  • Fix PS genotype field from octopus to have the correct type.
  • Edit VarDict headers to report VCFv4.2, since htsjdk does not fully support VCFv4.3 yet.
  • Attempt to speed up bismark by implementing the parallelization strategy suggested here: https://github.com/FelixKrueger/Bismark/issues/96
  • Add --enumerate option to OptiType to report the top 10 calls and scores, to make it easier to decide how confident we are in a HLA call.
  • Performance improvements when HLA calling during panel sequencing. This skips running bwa-kit during the initial mapping for consensus UMI detection, greatly speeding up panel sequencing runs.
  • Allow custom options to be passed to featureCounts.
  • Fix race condition when running tests.
  • Add TOPMed as a datatarget.
  • Add predicted transcript and peptide output to arriba.
  • Add mm10 as a supported genome for arriba.
  • Skip bcbioRNASeq for more than 100 samples.
  • Add rRNA_pseudogene as a rRNA biotype.
  • Add --genomicsdb-use-vcf-codec when running GenotypeGVCF. See https://gatk.broadinstitute.org/hc/en-us/articles/360040509751- GenotypeGVCFs#--genomicsdb-use-vcf-codec for a discussion. Thanks to @amizeranschi for finding the issue and posting the solution.
  • update VEP to v100
  • Add consensus peak calling using https://bedops.readthedocs.io/en/latest/content/usage-examples/master-list.html to collapse overlapping peaks.
  • Pre-filter consensus peaks by removing peaks with FDR > 0.05 before performing consensus peak calling.
  • Add support for Qiagen's Qiaseq UPX 3' transcriptome kit for DGE. Support for 96 and 384 well configurations by specifying umi_type: qiagen-upx-96 or umi_type: qiagen-upx-384.
  • Add consensus peak counting using featureCounts.
  • Skip using autosomal-reference when calling ataqv for mouse/human, as this has a problem with ataqv (see https://github.com/ParkerLab/ataqv/issues/10) for discussion and followup.
  • Add pre-generated ataqv HTML report to upload directory.
  • Support single-end reads for ATAC-seq.
  • Move featureCount output files to featureCounts directory in project directory.
  • Remove RNA and reads in peak stats from MultiQC table when they are not calculated for a pipeline.
  • Only show somatic variant counts in the general stats table, if germline variants are calculated.
  • Add kit parameter for setting options for pipelines via just listing the kit. Currently only implemented for WGBS.

Files

bcbio/bcbio-nextgen-v1.2.4.zip

Files (17.8 MB)

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Additional details

Related works

Is supplement to
https://github.com/bcbio/bcbio-nextgen/tree/v1.2.4 (URL)