bcbio-nextgen v0.7.0 Release Notes
Release Date: 2013-07-30 // over 10 years ago-
- ⚡️ RNA-seq pipeline updated: deprecate Tophat 1 in favor of Tophat 2. Perform automatic adapter trimming of common adapter sequences. STAR aligner support. RNA-SeQC support for RNA-seq specific quality control. Transcript quantitation with htseq-count.
- ⚡️ Updated installation and upgrade procedures, to make it easier to build an initial analysis pipeline and upgrade bcbio-nextgen and third-parts tools and data in place.
- ➕ Add support for MuTect tumor/normal variant caller, contributed by Luca Beltrame.
- 👍 Generalize variant calling to support alternative callers like cancer-specific calling: provide additional associated files to variant calls and pass along sample specific metadata. Document implementation of new variant callers.
- 👌 Improve algorithms around post-variant calling preparation. Avoid unnecessary tries for VQSR on low coverage whole genome reads, and concatenate VCF files to avoid locking penalties.
- 🛠 Fix logging and memory usage for multicore jobs run within ipython clusters.
- 👌 Improve logging for IPython cluster issues, including moving IPython logs inside project logging directory for better access.
- Options for improved cluster resiliency: minimize number of clusters started during processing with more extensive reuse, flexible timeouts for waiting on cluster start up, and expose options to allow job retries. Thanks to Zhengqiu Cai for suggestions and testing.