FAQ

How to report a bug or to ask a question?

The best way is: First, read the website thoroughly especially documentation (GMD; SMD) and FAQ. Second, if you cannot find answer or do not understand the answer well, please post an issue at the BitBucket issue tracking board (GMD; SMD). We prefer that was as it helps organize and track the questions. All of us watch the queue daily. Alternatively, you may contact our developers. Please include (1) which pipeline and its version (2) command line argument (3) error message (4) example input/config files if necessary (5) computer platform, Windows, Mac or Linux. Those information will help us diagnosis the issues promptly.

Which species does ExScalibur support?

The currently supported species are listed in Release. We are adding more species and assemblies (mm10, hg38) and it will be included in our next release.

Which aligners and callers does ExScalibur support?

The currently supported aligners and callers are listed in Release. We are adding more callers (e.g. VCMM) and will release an update soon. If there is any aligner/caller that you are interested in using in ExScalibur, please send us an email and we will be able to help you.

What is scatter-gather?

In ExScalibur pipelines, scatter-gather can be activated by switching on option [--split] while building the pipeline scripts. In "scatter-gather" mode, target regions will be split into even-sized bins and variants will be called from each bin. At the end, the pipeline will collect results of each bin and generate one complete set of variants for the whole exome. The "scatter-gather" mode speeds up the analysis considerably provided with sufficient computational resources. A nice description and examples of the "scatter-gather" concept can be found in GATK documentation.

I received error messages that bds can't be found. Why?

It is because bds is not in your system path. Please follow instructions on BigDataScript to add it to PATH.

I want to run ExScalibur on a different HPC/cloud. What should I do?

First, please download and install the pipelines following the instructions on Source (for HPC) and on Cloud (for cloud). Second, please obtain the information that which job scheduler is running on the HPC/cloud (by communicating to the system administrator or reading the documentation of HPC/cloud settings). For example, the ExScalibur image we created on AWS EC2 was built on StarCluster, which runs SGE as the scheduler. Third, you need to change the scheduler settings in bds config file located in MyInstallationPath/.bds/bds.config, following the instructions on BigDataScript. Fourth, install the required programs, software and libraries listed on Documentation. We recommend setting up Environmental Modules for each program/software, but that is optional. Lastly, update the path (or module name) of the program_exe variables in pipeline config file (more details on Documentation). Now, you are good to go!!

How to support ExScalibur?

If ExScalibur is helpful to your work or research, please cite it in your presentation slides, or in your published scientific manuscripts. That means a lot to us.

How to cite ExScalibur?

Our paper has been published on PLOS ONE. Please cite:
Bao R, Hernandez K, Huang L, Kang W, Bartom E, Onel K, et al. ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification. PloS one. 2015;10(8):e0135800. doi: 10.1371/journal.pone.0135800. PubMed PMID: 26271043.