GenPipes 4.4.0 Release Notes

What’s new?

This is a medium release with revamping of ‘sv’ protocol in the Tumor Pair pipeline and addition of a new protocol in the RNASeq pipeline.

  • Tumor Pair: ‘sv’ protocol updates

    • supports GRIDSS to detect genomics rearrangements and call structural variations

    • PURPLE adds information from the SV call to improve purity and ploidy estimates

    • supports Linx for structural variants annotation

  • RNA Sequencing Pipeline: - Newly added protocols:

    • ‘variants’ protocol provides support for small variant calling using GATK best practices

    • ‘cancer’ protocol provides support for:

    • Deprecated - the ‘cufflinks’ protocol is no longer supported

  • RNA Sequencing Light: - calls to kallisto quant are now aggregated by sample instead of by the readset

  • Overall, the job dependencies have been strengthened in GenPipes 4.4.0 release.

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

Where is the detailed ChangeLog?

A ChangeLog ( 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:

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