GenPipes release 4.2.0
edouard.henrion
A new release of the GenPipes, 4.2.0 is now available.
What's new?
==========
* New ini file setup with one common ini per cluster for all pipelines (found in pipeline/common_ini folder)
* ChIPSeq : added variant calling using GATK4
* Tumor Pair: fix of numerous bugs and departure from GEMINI to PCGR/CPSR reporting.
Info on the reporting system:
PCGR interprets primarily somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl's Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations retrieved flexibly through vcfanno, and produces interactive HTML reports intended for clinical interpretation. PCGR performs multiple types of analysis, including :
Somatic variant classification (ACMG/AMP)
mapping the therapeutic and prognostic implications of somatic DNA aberrations
Tumor mutational burden (TMB) estimation
Tumor-only analysis (variant filtering)
Mutational signature analysi
Kataegis detection
Microsatellite instability (MSI) classification
The accompanying tool CPSR is used to interrogate germline variants and their relation to cancer predisposition.
Where to find it?
============
* This version tarball is in bitbucket :
https://bitbucket.org/mugqic/genpipes/downloads/genpipes-4.2.0.tar.gz
* The module mugqic/genpipes/4.2.0 is installed on Abacus (MGC), Béluga, Graham, Cedar and Narval Compute Canada clusters.
* The source code is in bitbucket :
https://bitbucket.org/mugqic/genpipes
* For more documentation, please refer to :
https://genpipes.readthedocs.io/ (updates for 4.2.0 are coming soon)
Where is the detailed ChangeLog?
==========================
A ChangeLog (CHANGELOG.md) is available in the archive as well as in the repository.
Since we use git, there are many ways to get the details in many formats.
One of our preferred ways is to use a script written by the author of the Ray assembler: Sébastien Boisvert,
which lists the commits by tag and author:
https://raw.github.com/sebhtml/ray/master/scripts/dump-ChangeLog.sh
Regards,
Edouard