GenPipes 3.6.0 Release Notes

What’s new?

• The CovSeq Pipline has been updated:

  • Freebayes variant calling added in addition to ivar (Note: ivar was the only caller used in earlier versions)

  • Reporting step with ncov-tools usage on both freebayes and ivar consensus outputs

• Pipeline DNAseq updates :

  • Addition of VariantBam implementation for further space reduction of base re-calibrated crams

• Tumor Pair pipeline is back !

  • Use of GATK4 for bam processing and mutect2 is now default

  • Removal of samtools in ensemble protocol in favor of Strelka somatic and germline caller

  • Addition of newer purity estimate - purple

  • Improved behavior for WES data

  • Next to be improved : reporting system for somatic and germline calls

Quick! Where can I find it? I can’t wait!

• This version tarball is in: https://bitbucket.org/mugqic/genpipes/downloads/genpipes-3.6.0.tar.gz

• The module mugqic/genpipes/3.6.0 is installed on Abacus (MGC), Béluga, Graham and Cedar clusters.

• The source code is in bitbucket: https://bitbucket.org/mugqic/genpipes

• For more documentation, please refer to: https://genpipes.readthedocs.io/

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

Enjoy our pipelines on the many clusters where they are installed!