# clair3

## Summary

+ **Module Name:** clair3
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [clair3 github](https://github.com/HKU-BAL/clair3)

## Software Description

Clair3 is a germline small-variant caller for long-read sequencing. 

## General Usage

To see which modules are available for loading you can run:

`module avail clair3`

This will provide a list of all versions of the package, shown as clair3/<version>.

To load a specific module for use, run the command:

`module load clair3/<version>`

For example, you can use the command `module load clair3/b61ee22` to load version 2.0.0 
which is the current version available on our system.

To view the help menu after it is loaded, use the command:

`run_clair3.sh --help`

## Included models

The Clair3 module is installed as an apptainer, and has the following models included:

- hifi
- hifi_revio
- hifi_sequel2
- ilmn
- ont
- ont_guppy5
- r1041_e82_400bps_hac_v410
- r1041_e82_400bps_hac_v500
- r1041_e82_400bps_hac_with_mv
- r1041_e82_400bps_sup_v410
- r1041_e82_400bps_sup_v430_bacteria_finetuned
- r1041_e82_400bps_sup_v500
- r941_prom_hac_g360+g422
- r941_prom_sup_g5014

These models are in the path `/opt/Clair3/models`

Therefore, to specify, for example, the hifi_revio model, the correct argument
is:

`--model_path=/opt/Clair3/models/hifi_revio`


## Example SBATCH Script
The following is an example job script (clair3.sbatch) to which performs variant calling
using the ont model. Note that to use the ont model, we specify both the platform (ont) as
well as the specific model. The options for platform are ont, hifi, ilmn. The options for
the model are above. 

```
#!/bin/bash
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 12
#SBATCH --mem=128gb
#SBATCH -t 24:00:00
#SBATCH -p msismall
#SBATCH --mail-user=$USER@umn.edu
#SBATCH --mail-type=ALL
#SBATCH -e clair3_%j.err
#SBATCH -o clair3_%j.out

# load the module
module load clair3/b61ee22

# Change the following to match your project
INPUT_BAM="/path/to/your/input/bam"    # the path to your input bam file
REFERENCE="/path/to/reference/fasta"   # the path to the reference fasta file, e.g. from /common/bioref/ensembl
OUTPUTDIR="/path/to/where/output/goes" # the directory where output should go

# The actual command. Change the platform and model_path to match your project.
run_clair3.sh \
  --bam_fn="$INPUT_BAM" \
  --ref_fn="$REFERENCE" \
  --threads=12 \
  --platform=ont \
  --model_path="/opt/Clair3/models/ont" \
  --output="$OUTPUTDIR"

```