clair3
Link to section 'Introduction' of 'clair3' Introduction
Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
Docker hub: https://hub.docker.com/r/hkubal/clair3
Home page: https://github.com/HKU-BAL/Clair3
Link to section 'Versions' of 'clair3' Versions
- 0.1-r11
- 0.1-r12
Link to section 'Commands' of 'clair3' Commands
- run_clair3.sh
Link to section 'Module' of 'clair3' Module
You can load the modules by:
module load biocontainers
module load clair3
Model_path
model_path is in /opt/models/. The parameter will be like this --model_path="/opt/models/MODEL_NAME"
Link to section 'Example job' of 'clair3' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run clair3 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clair3
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers clair3
run_clair3.sh \
--bam_fn=input.bam \
--ref_fn=ref.fasta \
--threads=12 \
--platform=ont \
--model_path="/opt/models/ont" \
--output=output