1.0.9

Clair3 container

Main tool: clair3

Code repository: https://github.com/HKU-BAL/Clair3

Basic information on how to use this tool:

• executable: run_clair3.sh
• help: -h, --help
• version: -v, --version
• description:

Additional information:

This container includes models in /clair3/models

Full documentation: https://github.com/HKU-BAL/Clair3

Example Usage

run_clair3.sh \
  --bam_fn=${BAM} \
  --ref_fn=${REF} \
  --threads=${THREADS} \  		     
  --platform="ont" \               ## options: {ont,hifi,ilmn}
  --model_path=${MODEL_PREFIX} \   ## absolute model path prefix
  --output=${OUTPUT_DIR}           ## absolute output path prefix
## pileup output file: ${OUTPUT_DIR}/pileup.vcf.gz
## full-alignment output file: ${OUTPUT_DIR}/full_alignment.vcf.gz
## Clair3 final output file: ${OUTPUT_DIR}/merge_output.vcf.gz