Consequences of Expressed Variants Hackathon


The two-day “Consequences of Expressed Variants” hackathon will take place Wednesday Nov 18 and Thursday Nov 19th 2020. The goal of this hackathon is to construct end-to-end processing pipelines for cancer-related variant calling on RNA seq data! These pipelines may be constructed and tested on a number of platforms, including Bioconductor and GenePattern using publicly available data. After variants have been called, they can be annotated and evaluated using OpenCRAVAT and other variant annotators/platforms.

Potential topics include

  • Compound heterozygotes

  • Gene dosage

  • Differentiation of somatic variants from germline

  • Pleiotropy

  • Genome editing in single cell

  • Haplotype-specific expression

  • Pipelines that utilize multiple resources, such as Trinity-CTAT and StringTie


Participation will be open to any serious members of the bioinformatics community. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for genomic analyses. We particularly encourage participation of individuals from ITCR-funded projects, such as Trinity-CTAT, cBioPortal, and GenePattern. We welcome other participants who are algorithm developers in this space. Industry participants are also welcome.

Working groups of five to six individuals will be formed into five to eight teams. The projects will be unveiled before the hackathon starts, and will build off of previous community projects where possible. All pipelines and other scripts, software, and programs generated in this hackathon will be added to a public GitHub repository designed for that purpose (


Applicants can apply here and will be accepted on a rolling basis until Nov 6th, 2020. Participants will be selected based on the experience and motivation they provide on the form. Participants will need to bring their own laptop to this program. A working knowledge of scripting (e.g., Shell, Python, R) is useful but not necessary to be successful in this event. Applicants must be willing to commit to both days of the event. There will be no registration fee or cost associated with attending this event.

For more information, or with any questions, please contact Kym Pagel --