VCF Annotation Tools (VAtools) on Biowulf
VAtools is a python package that includes several tools to annotate VCF files with data from other tools.
Documentation
Important Notes
- Module Name: vatools (see the modules page for more information)
- singlethreaded
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load vatools [user@cn3144 ~]$ vcf-info-annotator -d test -f String old_test.vcf test.tsv test [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. vatools.sh). For example:
#!/bin/bash set -e module load vatools vcf-info-annotator -d test -f String old_test.vcf test.tsv test
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] vatools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. vatools.swarm). For example:
vcf-info-annotator -d test1 -f String old_test1.vcf test.tsv test1 vcf-info-annotator -d test2 -f String old_test2.vcf test.tsv test2 vcf-info-annotator -d test3 -f String old_test3.vcf test.tsv test3 vcf-info-annotator -d test4 -f String old_test4.vcf test.tsv test4
Submit this job using the swarm command.
swarm -f vatools.swarm [-g #] --module vatoolswhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module vatools | Loads the vatools module for each subjob in the swarm |