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.
Clair3 is the 3rd generation of Clair (the 2nd) and Clairvoyante (the 1st).
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