Deprecated: Use of this version of SAMtools is deprecated. More information on our Applications Support and Retention Policy.
There is a newer version of SAMtoolsSAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Accessing SAMtools 1.9-foss-2018b
To load the module for SAMtools 1.9-foss-2018b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):
module load SAMtools/1.9-foss-2018b
BEAR Apps Version
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 and CaStLeS Cloud 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.
For more information visit the SAMtools website.
This version of SAMtools has a direct dependency on: bzip2/1.0.6-GCCcore-7.3.0 foss/2018b ncurses/6.1-GCCcore-7.3.0 XZ/5.2.4-GCCcore-7.3.0 zlib/1.2.11-GCCcore-7.3.0
This version of SAMtools is a direct dependent of: AUGUSTUS/3.3.2-foss-2018b-Python-2.7.15 bam-readcount/0.8.0-foss-2018b HAPDeNovo/fe8bcc2-foss-2018b-Python-3.6.6 OptiType/1.3.2-foss-2018b-Python-3.6.6 OptiType/1.3.2-foss-2018b-Python-2.7.15 TraCeR/0.6.0-foss-2018b-Python-3.6.6 TRAPeS/e65bb7b-foss-2018b-Python-2.7.15
These versions of SAMtools are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.
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Last modified on 3rd June 2019