bcbio-nextgen v1.2.4 Release Notes

Release Date: 2020-09-21 // 2 months ago
  • 1.2.4 (21 September 2020)

    • โœ‚ Remove deprecated --genomicsdb-use-vcf-codec option as this is now the default.
    • โž• Add bismark output to MultiQC.
    • ๐Ÿ›  Fix PS genotype field from octopus to have the correct type.
    • ๐Ÿ‘ 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: FelixKrueger/Bismark#96
    • โž• 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.
    • ๐ŸŽ 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.
    • ๐Ÿ‘ Allow custom options to be passed to featureCounts.
    • ๐Ÿ›  Fix race condition when running tests.
    • โž• Add TOPMed as a datatarget.
    • โž• Add predicted transcript and peptide output to arriba.
    • โž• Add mm10 as a supported genome for arriba.
    • Skip bcbioRNASeq for more than 100 samples.
    • โž• Add rRNA_pseudogene as a rRNA biotype.
    • โž• 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.
    • โšก๏ธ update VEP to v100
    • โž• 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.
    • โž• 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.
    • โž• Add consensus peak counting using featureCounts.
    • Skip using autosomal-reference when calling ataqv for mouse/human, as this has a problem with ataqv
      ๐Ÿ‘€ (see ParkerLab/ataqv#10) for discussion and followup.
    • โž• Add pre-generated ataqv HTML report to upload directory.
    • ๐Ÿ‘Œ Support single-end reads for ATAC-seq.
    • ๐Ÿ”‹ Move featureCount output files to featureCounts directory in project directory.
    • โœ‚ 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.
    • โž• Add kit parameter for setting options for pipelines via just listing the kit. Currently only implemented for WGBS.

Previous changes from v1.2.3

    • ๐Ÿš‘ Hotfix for not being able to upgrade from stable distribution.