SOFT : Clair
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Site du soft: https://github.com/HKU-BAL/Clair
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LICENSE:
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BSD-3-Clause License

See software documentation for more informations.

Location: /usr/local/bioinfo/src/Clair
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Load binaries and environment:
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-> Version v2.1.1

#Need Miniconda
module load system/Miniconda3-4.7.10
module load bioinfo/Clair-v2.1.1

Be careful, to unload, not use module purge but in order:

module unload  bioinfo/Clair-v2.1.1
module unload system/Miniconda3-4.7.10

Pretrained models are here: /usr/local/bioinfo/src/Clair/Clair-v2.1.1/models/ (variable $CLAIR_MODELS is exported when module is load).
To use them:
export MODEL=$CLAIR_MODELS/<tech_folder>/model (where tech_folder is ont, illumina or pacbio). Ex for illumina model: export MODEL=$CLAIR_MODELS/illumina/model

To use your own model:
export MODEL=<path_to_model>

and
clair.py --chkpnt_fn $MODEL ...

-> Version 3-v0.1.12

#Need Miniconda
module load system/Miniconda3
module load bioinfo/Clair3-v0.1.12

Be careful, to unload, not use module purge but in order:

module unload bioinfo/Clair3-v0.1.12
module unload system/Miniconda3

run_clair3.sh ...

Pretrained models are here: /usr/local/bioinfo/src/Miniconda/Miniconda3/envs/Clair3-v0.1.12_env/bin/models/


Example directory for use on cluster:
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/usr/local/bioinfo/src/Clair/example_on_cluster

To submit: sbatch test_Clair-v2.1.1.sh or cd Clair3-v0.1.12 && sbatch test_Clair3-v0.1.12.sh

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.