VAtools is a python package that includes several tools to annotate VCF files with data from other tools.

• VATools Main Site

• Module Name: vatools (see the modules page for more information)
• singlethreaded

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 ~]$

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

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 vatools