bcbio-nextgen v1.2.5 Release Notes
Release Date: 2021-01-01 // about 3 years ago-
- Joint calling for RNA-seq variant calling requires setting
jointcaller
to bring it in line with the configuration options for variant calling. - ๐ Allow pre-aligned BAMs and gVCFs for RNA-seq joint variant calling. Thanks to @WimSpree for the feature.
- ๐ Allow
CollectSequencingArtifacts
to be turned off viatools_off: [collectsequencingartifacts]
. - ๐ Fix getiterator -> iter deprecation in ElementTree. Thanks to @smoe.
- โ Add SummarizedExperiment object from RNA-seq runs, a simplified version of the bcbioRNASeq object.
- โ Add
umi_type: dragen
. This enables bcbio to run with first-pass, pre-consensus called UMI BAM files from DRAGEN. - Turn off inferential replicate loading when creating the gene x sample RNA-seq count matrix. This allows loading of thousands of RNA-seq samples.
- Only make isoform to gene file from express if we have run express.
- ๐ Allow "no consensus peaks found" as a valid endpoint of a ChIP-seq analysis.
- โ
Allow
BCBIO_TEST_DIR
environment variable to control where tests end up. - Collect OxoG and other sequencing artifacts due to damage.
- Round tximport estimated counts.
- Turn off consensus peak calling for broad peaks. Thanks to @lbeltrame and @LMannarino for diagnosing the broad-peaks-run-forever bug.
- Joint calling for RNA-seq variant calling requires setting