Skip to content

v1.1.6
Compare
Choose a tag to compare
@roryk roryk released this 10 Oct 16:30
· 828 commits to master since this release
v1.1.6
f150184
  • GATK ApplyBQSRSpark: avoid StreamClosed issue with GATK 4.1+
  • RNA-seq: fixes for cufflinks preparation due to python3 transition.
  • RNA-seq: output count tables from tximport for genes and transcripts. These
    are in bcbioRNASeq/results/date/genes/counts and
    bcbioRNASeq/results/data/transcripts/counts.
  • qualimap (RNA-seq): disable stranded mode for qualimap, as it gives incorrect
    results with the hisat2 aligner and for RNA-seq just setting it to unstranded
  • Add quantify_genome_alignments option to use genome alignments to quantify
    with Salmon.
  • Add --validateMappings flag to Salmon read quantification mode.
  • VEP cache is not installing anymore from bcbio run
  • Add support for Salmon SA method when STAR alignments are not available
    (for hg38).
  • Add support for the new read model for filtering in Mutect2. This is
    experimental, and a little flaky, so it can optionally be turned on via:
    tools_on: mutect2_readmodel. Thanks to @lbeltrame for implementing this
    feature and doing a ton of work debugging.
  • Swap pandas from_csv call to read_csv.
  • Make STAR respect the transcriptome_gtf option.
  • Prefix regular expression with r. Thanks to @smoe for finding all of these.
  • Add informative logging messages at beginning of bcbio run. Includes the version
    and the configuration files being used.
  • Swap samtools mpileup to use bcftools mpileup as samtools mpileup is being
    deprecated (https://github.com/samtools/samtools/releases/tag/1.9).
  • Ensure locale is set to one supporting UTF-8 bcbio-wide. This may need to get
    reverted if it introduces issues.
  • Added hg38 support for STAR. We did this by taking hg38 and removing the alts,
    decoys and HLA sequences.
  • Added support for the arriba fusion caller.
  • Added back missing programs from the version provenance file. Fixed formatting
    problems introduced by switch to python3.
  • Added initial support for whole genome bisulfite sequencing using bismark. Thanks to
    @hackdna for implementing this and @jnhutchinson for drafting the initial
    pipeline. This is a work in progress in collaboration with @gcampanella, who
    has a similar implementation with some extra features that we will be merging
    in soon.
  • qualimap for RNA-seq runs on the downsampled BAM files by default. Set
    tools_on: [qualimap_full] to run on the full BAM files.
  • Add STAR junction files to the files captured at the end of a run.
Assets 2
Loading