bcbio-nextgen v1.1.9 Release Notes

Release Date: 2019-12-06 // about 2 months ago
    • 🛠 Fix for get VEP cache.
    • 👌 Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).
    • ✂ Remove mitochondrial reads from ChIP/ATAC-seq calling.
    • ➕ Add documentation describing ATAC-seq outputs.
    • ➕ Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report
      👀 (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics)
    • ➕ Add STAR sample-specific 2-pass. This helps assign a moderate number of reads per genes. Thanks
      to @naumenko-sa for the intial implementation and push to get this going.
    • 🛠 Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that
      can happen.
    • ➕ Add --buildversion option, for tracking which version of a gene build was used. This is used
      during bcbio_setup_genome.py. Suggested formats are source_version, so Ensembl_94,
      EnsemblMetazoa_25, FlyBase_26, etc.
    • Sort MACS2 bedgraph files before compressing. Thanks to @LMannarino for the suggestion.
    • 📇 Check for the reserved field sample in RNA-seq metadata and quit with a useful error message.
      Thanks to @marypiper for suggesting this.
    • 🆓 Split ATAC-seq BAM files into nucleosome-free and mono/di/tri nucleosome files, so we can call
      peaks on them separately.
    • Call peaks on NF/MN/DN/TN regions separately for each caller during ATAC-seq.
    • 👍 Allow viral contamination to be assasyed on non tumor/normal samples.
    • Ensure EBV coverage is calculated when run on genomes with it included as a contig.

Previous changes from v1.1.8

    • ➕ Add antibody configuration option. Setting a specific antibody for ChIP-seq will use appropriate
      📚 settings for that antibody. See the documentation for supported antibodies.
    • Add use_lowfreq_filter for forcing vardict to report variants with low allelic frequency,
      👉 useful for calling somatic variants in panels with high coverage.
    • 🛠 Fix for checking for pre-existing inputs with python3.
    • ➕ Add keep_duplicates option for ChIP/ATAC-seq which does not remove duplicates before peak calling.
      0️⃣ Defaults to False.
    • ➕ Add keep_multimappers for ChIP/ATAC-seq which does not remove multimappers before peak calling.
      0️⃣ Defaults to False.
    • ✂ Remove ethnicity as a required column in PED files.