cnvHiTSeq v0.1.2

cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input.

Accessing the software

To load the module:

$ module load apps/cnvhitseq/v0.1.2

An example command to include in your job script:

sh extract_region_from_BAM.sh "./input/test.bam" "./input/chr8_test.bam" "8:24000000-25000000"

The above command extracts chr8:24,000,000-25,000,000 from a local BAM file.

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 cnvHiTSeq website for more information regarding this application.


Last modified: 10 November 2017