Difference between revisions of "Vt"
(Created page with "== Description == ''From the {{PAGENAME}} Home Page:'' '''vt''' is a variant tool set that discovers short variants from Next Generation Sequencing data. The features are bei...") |
|||
(2 intermediate revisions by 2 users not shown) | |||
Line 5: | Line 5: | ||
{{AppStandardHeader|0.577|vt}} | {{AppStandardHeader|0.577|vt}} | ||
{{ | {{AppRunningOnAll}} | ||
=== Interactive Mode === | === Interactive Mode === | ||
Line 11: | Line 11: | ||
Next, use the following commands to open an [[SLURM Interactive|SRUN Interactive Session]], load the module for {{PAGENAME}}, and execute the {{PAGENAME}} binary: | Next, use the following commands to open an [[SLURM Interactive|SRUN Interactive Session]], load the module for {{PAGENAME}}, and execute the {{PAGENAME}} binary: | ||
<pre style="white-space:pre-wrap; width:75%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ srun --time=48:00:00 --nodes=1 -- | <pre style="white-space:pre-wrap; width:75%; border:1px solid lightgrey; background:#000000; color:white;">[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --cpus-per-task=1 --pty /bin/bash | ||
[user@wh-520-4-1 ~]$ module load apps/vt/0.577 | [user@wh-520-4-1 ~]$ module load apps/vt/0.577 | ||
[user@wh-520-4-1 ~]$ vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf | [user@wh-520-4-1 ~]$ vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf | ||
Line 18: | Line 18: | ||
=== Batch Job submission === | === Batch Job submission === | ||
To run batch jobs on the CIRCE cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than | 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 30 minutes to run on a standard PC. | ||
If, for example, you wish to normalize variants, send to standard out and remove duplicates, you would set up a submit script to use vt like this | If, for example, you wish to normalize variants, send to standard out and remove duplicates, you would set up a submit script to use vt like this |
Latest revision as of 15:32, 13 March 2023
Description
From the Vt Home Page: vt is a variant tool set that discovers short variants from Next Generation Sequencing data. The features are being rolled out to github as major rewriting is being undertaken.
Version
- 0.577
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
Vt requires the following module file to run:
apps/vt/0.577
- See Modules for more information.
Running Vt on CIRCE/SC
The Vt 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 $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Interactive Mode
Next, use the following commands to open an SRUN Interactive Session, load the module for Vt, and execute the Vt binary:
[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --cpus-per-task=1 --pty /bin/bash [user@wh-520-4-1 ~]$ module load apps/vt/0.577 [user@wh-520-4-1 ~]$ vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf
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 30 minutes to run on a standard PC.
If, for example, you wish to normalize variants, send to standard out and remove duplicates, you would set up a submit script to use vt like this
#!/bin/bash # #SBATCH --job-name=vt-test #SBATCH --time=01:00:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --output=output.%j.vt-test #### SLURM 1 processor vt test to run for 1 hours. # Load the vt module: module load apps/vt/0.577 # Start vt vt normalize dbsnp.vcf -r seq.fa | vt uniq - -o dbsnp.normalized.uniq.vcf
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 ./vt-test.sh
- You can view the status of your job with the “squeue -u <username>” command
Documentation
Home Page, User Guides, and Manuals
- Vt Home Page:
- Vt Documentation:
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with Vt to the IT Help Desk: rc-help@usf.edu