TVC is the standalone Torrent Variant Caller, part of the Ion Torrent Suite.

• TVC Main Site: Ion Community, at ThermoFisher Scientific
• Type variant_caller_pipeline.py without any arguments.

• Module Name: TVC (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• Environment variables set
  • PATH
  • TVC_ROOT_DIR
• Example files in $TVC_ROOT_DIR/share

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --mem=20g --cpus-per-task=16
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 TVC
[user@cn3144 ~]$ variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. TVC.sh). For example:

#!/bin/bash
module load TVC
variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=20g TVC.sh

Create a swarmfile (e.g. TVC.swarm). For example:

mkdir outdir1 ; variant_caller_pipeline.py -i /path/to/input1.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir1
mkdir outdir2 ; variant_caller_pipeline.py -i /path/to/input2.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir2
mkdir outdir3 ; variant_caller_pipeline.py -i /path/to/input3.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir3
mkdir outdir4 ; variant_caller_pipeline.py -i /path/to/input4.bam -r /path/to/reference/file.fasta -N $SLURM_CPUS_PER_TASK -o outdir4

NOTE: By default, all output is written in the current working directory. When run in a swarm, it is ideal to create a directory for the output and redirect that output using the -o option. This will prevent overwriting the same file by indendent swarm subjobs.

Submit this job using the swarm command.

swarm -f TVC.swarm -g 10 -t 8 --module TVC