TVC is the standalone Torrent Variant Caller, part of the Ion Torrent Suite.
There are multiple versions of TVC available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail TVC
To select a module, type
module load TVC/[ver]
where [ver] is the version of choice.
Environment variables set:
- $PATH
- $TVC_ROOT_DIR
Sample session:
$ module load TVC $ variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N [NUMTHREADS]
NOTE: The default number of threads ([NUMTHREADS]) is 12.
Create a batch input file (e.g. TVC.sh), which uses the input file 'input.bam'. For example:
#!/bin/bash module load TVC variant_caller_pipeline.py -i /path/to/input.bam -r /path/to/reference/file.fasta -N [NUMTHREADS]
Submit this job using the Slurm sbatch command.
$ sbatch --cpus-per-task=12 --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 8 -o outdir1 mkdir outdir2 ; variant_caller_pipeline.py -i /path/to/input2.bam -r /path/to/reference/file.fasta -N 8 -o outdir2 mkdir outdir3 ; variant_caller_pipeline.py -i /path/to/input3.bam -r /path/to/reference/file.fasta -N 8 -o outdir3 mkdir outdir4 ; variant_caller_pipeline.py -i /path/to/input4.bam -r /path/to/reference/file.fasta -N 8 -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 -t 8 -g 20
Once an interactive job has been started,
sinteractive --cpus-per-task=8 --mem=20g
load the module and run the command.
- TVC Main Site: Ion Community, at ThermoFisher Scientific
- Type variant_caller_pipeline.py without any arguments.
