Samtools

Description

From the Samtools Home Page: Tools (written in C using htslib) for manipulating next-generation sequencing data

Version

  • 1.3.1

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Samtools requires the following module file to run:

  • apps/samtools/1.3.1

Running Samtools on CIRCE/SC

The Samtools user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for Samtools, and execute the Samtools binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/samtools/1.3.1
[user@wh-520-4-1 ~]$ samtools view -C -T ref.fa aln.bam > aln.cram

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you have wish to convert a BAM file to a CRAM file using a local reference sequence, you would set up a submit script to use samtools like this

#!/bin/bash
#
#SBATCH --job-name=samtools-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.samtools-test

#### SLURM 1 processor bamtools test to run for 1 hours.

# Load the bamtools module:
module load apps/samtools/1.3.1

# Start samtools
samtools view -C -T ref.fa aln.bam > aln.cram

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./samtools-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Samtools to the IT Help Desk: rc-help@usf.edu