v1.1.9

• 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.

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.
  Defaults to False.
• Add keep_multimappers for ChIP/ATAC-seq which does not remove multimappers before peak calling.
  Defaults to False.
• Remove ethnicity as a required column in PED files.

v1.1.7

1.1.7

• hot fix for dataclasses not being supported in 3.6. Use namedtuple instead.

v1.1.6

• 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.