bcbio/bcbio-nextgen: v1.1.9

Published December 6, 2019 | Version v1.1.9

Software Open

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.

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bcbio/bcbio-nextgen-v1.1.9.zip md5:9ef59b0c6395d6b09459ee9a8e885074	17.8 MB	Preview Download