Clair3 is a small variant caller for Illumina, PacBio and ONT long reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster.

• Clair3 Github / tutorial page
• Training data and trained models
• Demos for processing Illumina, PacBio and ONT data

• Module Name: Clair3 (see the modules page for more information)
• Multithreaded
• Can be run on both CPU and GPU nodes
• Unusual environment variables set
  • CLAIR3_HOME  installation directory
  • CLAIR3_BIN       executable directory
  • CLAIR3_MODELS    trained models folder
  • CLAIR3_DATA    sample data folder

Allocate an interactive session and run the program.
Sample session on a GPU node:

[user@biowulf ~]$ sinteractive --gres=gpu:p100:1,lscratch:10 --mem=16g -c4
[user@cn2379 ~]$ module load clair3
[user@cn2379 ~]$ cp -r $CLAIR3_DATA/* .

[user@cn2379 ~]$ THREADS=4
[user@cn2379 ~]$ OUTPUT_VCF_FILE_PATH=merge_output.vcf.gz

 
[user@cn2379 ~]$ PLATFORM='ilmn' 
[user@cn2379 ~]$ INPUT_DIR="Illumina"
[user@cn2379 ~]$ cp -r $CLAIR3_DATA/${INPUT_DIR} .
[user@cn2379 ~]$ REF="GRCh38_chr20.fa"
[user@cn2379 ~]$ BAM="HG003_chr20_demo.bam"
[user@cn2379 ~]$ BASELINE_VCF_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark.vcf.gz"
[user@cn2379 ~]$ BASELINE_BED_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark_noinconsistent.bed"
[user@cn2379 ~]$ clair3 \
  --bam_fn=${INPUT_DIR}/${BAM} \
  --ref_fn=${INPUT_DIR}/${REF} \
  --model_path=${CLAIR3_MODELS}/${PLATFORM} \
  --threads=${THREADS} \
  --platform=${PLATFORM} \
  --output=./ \
  --bed_fn=${INPUT_DIR}/${BASELINE_BED_FILE_PATH} 
...

[user@cn2379 ~]$ PLATFORM='hifi' 
[user@cn2379 ~]$ INPUT_DIR="PacBio"
[user@cn2379 ~]$ cp -r $CLAIR3_DATA/${INPUT_DIR} .
[user@cn2379 ~]$ REF="GRCh38_no_alt_chr20.fa"
[user@cn2379 ~]$ BAM="HG003_chr20_demo.bam"
[user@cn2379 ~]$ BASELINE_VCF_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark.vcf.gz"
[user@cn2379 ~]$ BASELINE_BED_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark_noinconsistent.bed"
[user@cn2379 ~]$ clair3 \
  --bam_fn=${INPUT_DIR}/${BAM} \
  --ref_fn=${INPUT_DIR}/${REF} \
  --threads=${THREADS} \
  --platform=${PLATFORM} \
  --model_path=${CLAIR3_MODELS}/${PLATFORM} \
  --output=./ \
  --bed_fn=${INPUT_DIR}/${BASELINE_BED_FILE_PATH} 
...

[user@cn2379 ~]$ PLATFORM='ont' 
[user@cn2379 ~]$ INPUT_DIR="ONT"
[user@cn2379 ~]$ cp -r $CLAIR3_DATA/${INPUT_DIR} .
[user@cn2379 ~]$ REF="GRCh38_no_alt_chr20.fa"
[user@cn2379 ~]$ BAM="HG003_chr20_demo.bam"
[user@cn2379 ~]$ BASELINE_VCF_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark.vcf.gz"
[user@cn2379 ~]$ BASELINE_BED_FILE_PATH="HG003_GRCh38_chr20_v4.2.1_benchmark_noinconsistent.bed"
[user@cn2379 ~]$ clair3 \
  --bam_fn=${INPUT_DIR}/${BAM} \
  --ref_fn=${INPUT_DIR}/${REF} \
  --threads=${THREADS} \
  --platform=${PLATFORM} \                                                                            --model_path=${CLAIR3_MODELS}/${PLATFORM} \
  --output=./ \
  --vcf_fn=${INPUT_DIR}/${BASELINE_VCF_FILE_PATH} 
...

#!/bin/bash
set -e
module load Clair3 
...               
clair3 \ 
  --bam_fn=${INPUT_DIR}/${BAM} \
  --ref_fn=${INPUT_DIR}/${REF} \                                                                      --threads=${THREADS} \
  --platform=${PLATFORM} \                                                                            --model_path=${CLAIR3_MODELS}/${PLATFORM} \
  --output=./ \
  --vcf_fn=${INPUT_DIR}/${BASELINE_VCF_FILE_PATH}

sbatch clair3.sh