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| # Clair3 - Integrating pileup and full-alignment for high-performance long-read variant calling | ||
| # Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling | ||
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| [](https://opensource.org/licenses/BSD-3-Clause) [](http://bioconda.github.io/recipes/clair3/README.html) | ||
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| ## Introduction | ||
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| Clair3 is a small variant caller for 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 makes the best of both worlds of using pileup or full-alignment as input for deep-learning based long-read small variant calling. Clair3 is simple and modular for easy deployment and integration. | ||
| 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. | ||
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| Clair3 is the 3<sup>rd</sup> generation of [Clair](https://github.com/HKU-BAL/Clair) (the 2<sup>nd</sup>) and [Clairvoyante](https://github.com/aquaskyline/Clairvoyante) (the 1<sup>st</sup>). | ||
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| A short preprint describing Clair3's algorithms and results is at [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.12.29.474431v1). | ||
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| ---- | ||
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| ## We are working on ... | ||
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| * An ONT Guppy 5 model for production use will be released in mid January. | ||
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| ---- | ||
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| ## Contents | ||
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| * [Introduction](#introduction) | ||
| * [Latest Updates](#latest-updates) | ||
| * [Pre-trained Models](#pre-trained-models) | ||
| * [Guppy5 Model](docs/guppy5_20220113.md) | ||
| * [Guppy3-4 Model](#pre-trained-models) | ||
| * [Guppy5 Model](docs/guppy5.md) | ||
| * [Guppy2 Model](docs/guppy2.md) | ||
| * [ONT-provided Models](#ont-provided-models) | ||
| * [What's New in Clair3](#whats-new-in-clair3) | ||
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| ## Latest Updates | ||
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| *v0.1-r10 (Jan 13)* : 1. Added a new ONT Guppy5 model (`r941_prom_sup_g5014`). Click [here](docs/guppy5_20220113.md) for some benchmarking results. This `sup` model is also applicable to reads called using the `hac` and `fast` mode. The old `r941_prom_sup_g506` model that was fine-tuned from the Guppy3,4 model is obsoleted. 2. Added `--var_pct_phasing` option to control the percentage of top ranked heterozygous pile-up variants used for WhatsHap phasing. | ||
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| *v0.1-r9 (Dec 1)* : Added the `--enable_long_indel` option to output indel variant calls >50bp ([#64](https://github.com/HKU-BAL/Clair3/issues/64)), Click [here](https://github.com/HKU-BAL/Clair3/blob/main/docs/indel_gt50_performance.md) to see more benchmarking results. | ||
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| *v0.1-r8 (Nov 11)* : 1. Added the `--enable_phasing` option that adds a step after Clair3 calling to output variants phased by WhatsHap ([#63](https://github.com/HKU-BAL/Clair3/issues/63)). 2. Fixed unexpected program termination on successful runs. | ||
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| In a docker installation, models are in `/opt/models/`. In a bioconda installation, models are in `{CONDA_PREFIX}/bin/models/`. | ||
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| | Model name | Platform | Training samples | Included in the bioconda package | Included in the docker image | Release | Date | Basecaller | File | Link | | ||
| | :--------------------------: | :---------: | :----------------------------------------------------------: | -------------------------------- | :--------------------------: | :-----: | :------: | :--------: | ----------------------------------- | :----------------------------------------------------------: | | ||
| | r941_prom_hac_g360+g422 | ONT | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | Guppy3,4 | r941_prom_hac_g360+g422.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g360+g422.tar.gz) | | ||
| | r941_prom_hac_g360+g422_1235 | ONT | HG001,2,3,5 | | | 1 | 20210517 | Guppy3,4 | r941_prom_hac_g360+g422_1235.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g360+g422_1235.tar.gz) | | ||
| | r941_prom_sup_g506 | ONT | Base model: HG001,2,4,5 (Guppy3,4) <br>Fine-tuning data: HG002 (Guppy5_sup) | Yes | Yes | 1 | 20210609 | Guppy5 | r941_prom_sup_g506.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_sup_g506.tar.gz) | | ||
| | r941_prom_hac_g238 | ONT | HG001,2,3,4 | | Yes | 1 | 20210627 | Guppy2 | r941_prom_hac_g238.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g238.tar.gz) | | ||
| | hifi | PacBio HiFi | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | NA | hifi.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/hifi.tar.gz) | | ||
| | ilmn | Illumina | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | NA | ilmn.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/ilmn.tar.gz) | | ||
| | Model name | Platform | Training samples | Included in the bioconda package | Included in the docker image | Release | Date | Basecaller | File | Link | | ||
| | :----------------------------: | :---------: | :----------------------------------------------------------: | -------------------------------- | :--------------------------: | :-----: | :------: | :----------: | ----------------------------------- | :----------------------------------------------------------: | | ||
| | r941_prom_sup_g5014 | ONT | HG002,4,5 (Guppy5_sup) | Yes | Yes | 1 | 20220112 | Guppy5 sup | r941_prom_sup_g5014.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_sup_g5014.tar.gz) | | ||
| | r941_prom_hac_g360+g422 | ONT | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | Guppy3,4 hac | r941_prom_hac_g360+g422.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g360+g422.tar.gz) | | ||
| | r941_prom_hac_g360+g422_1235 | ONT | HG001,2,3,5 | | | 1 | 20210517 | Guppy3,4 hac | r941_prom_hac_g360+g422_1235.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g360+g422_1235.tar.gz) | | ||
| | r941_prom_hac_g238 | ONT | HG001,2,3,4 | | Yes | 1 | 20210627 | Guppy2 | r941_prom_hac_g238.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g238.tar.gz) | | ||
| | r941_prom_sup_g506 (obsoleted) | ONT | Base model: HG001,2,4,5 (Guppy3,4) <br>Fine-tuning data: HG002 (Guppy5_sup) | | | 1 | 20210609 | Guppy5 sup | r941_prom_sup_g506.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_sup_g506.tar.gz) | | ||
| | hifi | PacBio HiFi | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | NA | hifi.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/hifi.tar.gz) | | ||
| | ilmn | Illumina | HG001,2,4,5 | Yes | Yes | 1 | 20210517 | NA | ilmn.tar.gz | [Download](http://www.bio8.cs.hku.hk/clair3/clair3_models/ilmn.tar.gz) | | ||
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| #### ONT-provided Models | ||
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| # install python packages in environment | ||
| pip3 install tensorflow==2.2.0 | ||
| pip3 tensorflow-addons==0.11.2 tables==3.6.1 | ||
| pip3 install tensorflow-addons==0.11.2 tables==3.6.1 | ||
| conda install -c anaconda pigz==2.4 -y | ||
| conda install -c conda-forge parallel=20191122 zstd=1.4.4 -y | ||
| conda install -c conda-forge -c bioconda samtools=1.10 -y | ||
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| --indel_min_af=FLOAT Minimum INDEL AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.15,hifi:0.08,ilmn:0.08. | ||
| --var_pct_full=FLOAT EXPERIMENTAL: Specify an expected percentage of low quality 0/1 and 1/1 variants called in the pileup mode for full-alignment mode calling, default: 0.3. | ||
| --ref_pct_full=FLOAT EXPERIMENTAL: Specify an expected percentage of low quality 0/0 variants called in the pileup mode for full-alignment mode calling, default: 0.3 for ilmn and hifi, 0.1 for ont. | ||
| --var_pct_phasing=FLOAT EXPERIMENTAL: Specify an expected percentage of high quality 0/1 variants used in WhatsHap phasing, default: 0.8 for ont guppy5 and 0.7 for other platforms. | ||
| --pileup_model_prefix=STR EXPERIMENTAL: Model prefix in pileup calling, including $prefix.data-00000-of-00002, $prefix.data-00001-of-00002 $prefix.index. default: pileup. | ||
| --fa_model_prefix=STR EXPERIMENTAL: Model prefix in full-alignment calling, including $prefix.data-00000-of-00002, $prefix.data-00001-of-00002 $prefix.index, default: full_alignment. | ||
| --fast_mode EXPERIMENTAL: Skip variant candidates with AF <= 0.15, default: disable. | ||
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