Isaac Caller 1.0.7

Isaac Variant Caller (IVC) is an analysis package designed to detect SNVs and small indels from the aligned sequencing reads of a single diploid sample.

Note: There is no support or ongoing development for the Isaac Variant Caller package, please instead see the ongoing updates to germline-calling in Strelka2, featuring substantially improved accuracy, GPLv3 source licensing, multi-sample support and more.

Accessing the software

To load the module:

$ module load apps/isaac-caller/1.0.7

To view a list of command-line options, run the following command:

$ configureWorkflow.pl

Example: Isaac Caller Job

An example can be found at ${BB_EXAMPLES}/isaac-caller/1.0.7/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/isaac-caller/1.0.7 ~/isaac-caller-1.0.7-test
$ cd ~/isaac-caller-1.0.7-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the Isaac Caller Github repository for more information regarding this application.


Last modified: 14 September 2017