bcbio-nextgen v1.1.9 Release Notes
Release Date: 2019-12-06 // over 4 years ago-
- ๐ Fix for get VEP cache.
- ๐ Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY).
- โ Remove mitochondrial reads from ChIP/ATAC-seq calling.
- โ Add documentation describing ATAC-seq outputs.
- โ Add ENCODE library complexity metrics for ATAC/ChIP-seq to MultiQC report
๐ (see https://www.encodeproject.org/data-standards/terms/#library for a description of the metrics) - โ 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. - ๐ Index transcriptomes only once for pseudo/quasi aligner tools. This fixes race conditions that
can happen. - โ Add --buildversion option, for tracking which version of a gene build was used. This is used
duringbcbio_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.
- ๐ Check for the reserved field
sample
in RNA-seq metadata and quit with a useful error message.
Thanks to @marypiper for suggesting this. - ๐ 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.
- ๐ 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.