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.
A short pre-print describing Clair3's algorithms and results is at bioRxiv.
License and Disclaimer
Copyright 2021 The University of Hong Kong, Department of Computer Science
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Example Slurm script
Caution: Absolute path is needed for both
#SBATCH --account nesi12345
#SBATCH --job-name cliar3_job
#SBATCH --mem 6G #12G is just a place holder. Adjust accordingly
#SBATCH --cpus-per-task 4 #4 just a place holder. Adjust accordingly
#SBATCH --time 01:00:00
#SBATCH --output slurmout.%j.out
#Caution: Absolute path is needed for both INPUT_DIR and OUTPUT_DIR
INPUT_DIR=/path/to/input/data # e.g. /nesi/nobackup/nesi12345/input (absolute path needed)
OUTPUT_DIR=/path/to/save/outputs # /nesi/nobackup/nesi12345/output (absolute path needed)
REF=/path/to/reference/genomes # use the suggested Slurm variable which will read the value from `--cpus-per-task`
MODEL_NAME=/model/name # e.g. r941_prom_hac_g360+g422
module load Clair3/0.1.12-Miniconda3