OncoSNP-Seq 2.01

OncoSNP-SEQ is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.

Accessing OncoSNP-Seq 2.01

To load the module for OncoSNP-Seq 2.01 please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load OncoSNP-Seq/2.01

BEAR Apps Version

2020a

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR Cloud and CaStLeS VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

Using OncoSNP-Seq

To run this application, issue the following command:

run_oncoseq.sh ${MCRROOT} [options]

More Information

For more information visit the OncoSNP-Seq website.

Dependencies

This version of OncoSNP-Seq has a direct dependency on: MCR/R2013b

Last modified on 20th May 2019