Clair3-Trio: variant calling in trio using Nanopore long-reads

Contact: Ruibang Luo, Junhao Su
Email: rbluo@cs.hku.hk, jhsu@cs.hku.hk

Clair3-Trio is archived. Please visit the new version Clair3-Nova that extended Clair3-Trio to support accurate de novo variant calling.

Introduction

Accurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio’s predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods.

Detailed descriptions of the methodology and results for Clair3-Trio are available in this paper.

Latest Updates

v0.7.1 (Oct 17, 2023): Fix memory error issue.

v0.7 (July 9, 2023): Added the source/version/command tag into the VCF header. Fixed a bug of AF for 1/2 genotypes. Added AD into VCF output. Added document for output files. Added a page for the method of merging VCF.

v0.6 (April 25, 2023): Bumped up Python from 3.6 to 3.9, Whatshap from v1.0 to v1.7 Clair3 #193. Fixed gVCF format mistake #3. Added options "--enable_phasing", "--enable_output_phasing", and "enable_output_haplotagging" #4. Added singularity support.

v0.5 (April 10, 2023): Added support for gVCF output. Use --gvcf to enable gVCF output.

v0.4 (March 22, 2023): Added a model for R10.4 pore with the Kit 14 chemistry (Q20+). Check this page for more information about the model.

v0.3 (June 20, 2022): Optimized Clair3-Trio speed, the runtime of Clair3-Trio to call variants from the whole genome is about 2.4 times of calling a single sample form Clair3 (v0.1-r10).

v0.2 (May 15, 2022): A guppy5 model for Clair3-Trio is available now. Check this page for more information about the Guppy5 model.

v0.1 (April 22, 2022): Initial release.

What's New in Clair3-Trio

New Architecture. Clair3-Trio employs a Trio-to-Trio deep neural network model that allows it to take three samples as input and output the varaints of all three samples in one go.
Mendelian violations aware. Clair3-Trio uses MCVLoss to improve variants calling in trio by penalizing mendelian violoations.
Improved Performance. Using only 10x of HG002, 3 and 4 ONT data, Clair3-Trio achieved 97.30% SNP F1-score and 56.48% Indel F1-score. Compared to Clair3, Clair3-Trio reduced SNP errors by ~78%, and Indel errors by ~22%. Clair3-Trio signficantly reduced Mendelian violations from 48,345 to 7,072.

Pre-trained Models

Download models from here or click on the links below.

Model name	Platform	Training samples	Date	Basecaller	File	Link
c3t_hg002_dna_r1041_e82_400bps_sup	ONT 10.4.1	HG002,3,4	20230322	Dorado v4.0.0 SUP	c3t_hg002_dna_r1041_e82_400bps_sup.tar.gz	Download
c3t_hg002_r941_prom_sup_g5014	ONT r9.4.1	HG002,3,4	20220514	Guppy5 sup	c3t_hg002_r941_prom_sup_g5014.tar.gz	Download
c3t_hg002_g422	ONT r9.4.1	HG002,3,4	20220422	Guppy4 hac	c3t_hg002_g422.tar.gz	Download

Clair3's Pre-trained Models

When using the Clair3-Trio model, please use a corresponding Clair3 model for Pileup calling. Check here or here for more information about Clair3 pretrained model.

Model name	Platform	Training samples	Date	Basecaller	File	Link
r1041_e82_400bps_sup_v400	ONT r10.4.1	HG002,4,5	-	Dorado v4.0.0 SUP	r1041_e82_400bps_sup_v400.tar.gz	Download
r941_prom_sup_g5014	ONT r9.4.1	HG002,4,5 (Guppy5_sup)	20220112	Guppy5 sup	r941_prom_sup_g5014.tar.gz	Download
r941_prom_hac_g360+g422	ONT r9.4.1	HG001,2,4,5	20210517	Guppy3,4 hac	r941_prom_hac_g360+g422.tar.gz	Download

Quick Demo

see Trio Quick Demo.

Installation

Option 1. Docker pre-built image

A pre-built docker image is available here. With it you can run Clair3-Trio using a single command.

Caution: Absolute path is needed for both INPUT_DIR and OUTPUT_DIR.

INPUT_DIR="[YOUR_INPUT_FOLDER]"            # e.g. /input
REF=${_INPUT_DIR}/ref.fa                   # change your reference file name here
OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"          # e.g. /output
THREADS="[MAXIMUM_THREADS]"                # e.g. 8
MODEL_C3="[Clair3 MODEL NAME]"         	   # e.g. Clair3 model, r941_prom_hac_g360+g422 for Guppy4 data, r941_prom_sup_g5014 for Guppy5 data
MODEL_C3T="[Clair3-Trio MODEL NAME]"       # e.g. Clair3-Trio model, c3t_hg002_g422 for Guppy4 data, c3t_hg002_r941_prom_sup_g5014 for Guppy5 data


docker run -it \
  -v ${INPUT_DIR}:${INPUT_DIR} \
  -v ${OUTPUT_DIR}:${OUTPUT_DIR} \
  hkubal/clair3-trio:latest \
  /opt/bin/run_clair3_trio.sh \
  --ref_fn=${INPUT_DIR}/ref.fa \                  ## change your reference file name here
  --bam_fn_c=${INPUT_DIR}/child_input.bam \       ## change your child's bam file name here 
  --bam_fn_p1=${INPUT_DIR}/parent1_input.bam \    ## change your parent-1's bam file name here     
  --bam_fn_p2=${INPUT_DIR}/parenet2_input.bam \   ## change your parent-2's bam file name here   
  --sample_name_c=${SAMPLE_C} \                   ## change your child's name here
  --sample_name_p1=${SAMPLE_P1} \                 ## change your parent-1's name here
  --sample_name_p2=${SAMPLE_P2} \                 ## change your parent-2's name here
  --threads=${THREADS} \                          ## maximum threads to be used
  --model_path_clair3="/opt/models/clair3_models/${MODEL_C3}" \
  --model_path_clair3_trio="/opt/models/clair3_trio_models/${MODEL_C3T}" \
  --output=${OUTPUT_DIR}                          ## absolute output path prefix

Option 2. Singularity

Caution: Absolute path is needed for both INPUT_DIR and OUTPUT_DIR.

INPUT_DIR="[YOUR_INPUT_FOLDER]"            # e.g. /input
REF=${_INPUT_DIR}/ref.fa                   # change your reference file name here
OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"          # e.g. /output
THREADS="[MAXIMUM_THREADS]"                # e.g. 8
MODEL_C3="[Clair3 MODEL NAME]"         	   # e.g. Clair3 model, r941_prom_hac_g360+g422 for Guppy4 data, r941_prom_sup_g5014 for Guppy5 data
MODEL_C3T="[Clair3-Trio MODEL NAME]"       # e.g. Clair3-Trio model, c3t_hg002_g422 for Guppy4 data, c3t_hg002_r941_prom_sup_g5014 for Guppy5 data

conda config --add channels defaults
conda create -n singularity-env -c conda-forge singularity -y
conda activate singularity-env

# singularity pull docker pre-built image
singularity pull docker://hkubal/clair3-trio:latest

singularity exec \
-B ${INPUT_DIR},${OUTPUT_DIR} \
clair3-trio_latest.sif \
/opt/bin/run_clair3_trio.sh \
--ref_fn=${INPUT_DIR}/ref.fa \                  ## change your reference file name here
--bam_fn_c=${INPUT_DIR}/child_input.bam \       ## change your child's bam file name here 
--bam_fn_p1=${INPUT_DIR}/parent1_input.bam \    ## change your parent-1's bam file name here     
--bam_fn_p2=${INPUT_DIR}/parenet2_input.bam \   ## change your parent-2's bam file name here   
--sample_name_c=${SAMPLE_C} \                   ## change your child's name here
--sample_name_p1=${SAMPLE_P1} \                 ## change your parent-1's name here
--sample_name_p2=${SAMPLE_P2} \                 ## change your parent-2's name here
--threads=${THREADS} \                          ## maximum threads to be used
--model_path_clair3="/opt/models/clair3_models/${MODEL_C3}" \
--model_path_clair3_trio="/opt/models/clair3_trio_models/${MODEL_C3T}" \
--output=${OUTPUT_DIR}                          ## absolute output path prefix

Option 3. Build an anaconda virtual environment

Anaconda install:

Please install anaconda using the official guide or using the commands below:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x ./Miniconda3-latest-Linux-x86_64.sh 
./Miniconda3-latest-Linux-x86_64.sh

Install Clair3 env and Clair3-Trio using anaconda step by step:

# create and activate an environment named clair3
conda create -n clair3 python=3.9.0 -y
source activate clair3

# install pypy and packages in the environemnt
conda install -c conda-forge pypy3.6 -y
pypy3 -m ensurepip
pypy3 -m pip install mpmath==1.2.1

# install python packages in environment
conda install -c conda-forge tensorflow==2.8.0 -y
conda install -c conda-forge pytables -y
conda install -c anaconda pigz cffi==1.14.4 -y
conda install -c conda-forge parallel=20191122 zstd -y
conda install -c conda-forge -c bioconda samtools=1.15.1 -y
conda install -c conda-forge -c bioconda whatshap=1.7 -y
conda install -c conda-forge xz zlib bzip2 automake curl -y
# tensorflow-addons is required in training
pip install tensorflow-addons

# clone Clair3-Trio
git clone https://github.com/HKU-BAL/Clair3-Trio.git
cd Clair3-Trio

# download Clair3's pre-trained models
mkdir -p models/clair3_models
wget http://www.bio8.cs.hku.hk/clair3_trio/clair3_models/clair3_models.tar.gz 
tar -zxvf clair3_models.tar.gz -C ./models/clair3_models


# download Clair3-Trio's pre-trained models
mkdir -p models/clair3_trio_models
wget http://www.bio8.cs.hku.hk/clair3_trio/clair3_trio_models/clair3_trio_models.tar.gz 
tar -zxvf clair3_trio_models.tar.gz -C ./models/clair3_trio_models


# run clair3-trio
_INPUT_DIR="[YOUR_INPUT_FOLDER]"            # e.g. ./input
_BAM_C=${_INPUT_DIR}/input_child.bam        # chnage your child's bam file name here
_BAM_P1=${_INPUT_DIR}/input_parent1.bam     # chnage your parent-1's bam file name here
_BAM_P2=${_INPUT_DIR}/input_parent2.bam     # chnage your parent-2's bam file name here
_SAMPLE_C="[Child sample ID]"               # child sample ID, e.g. HG002
_SAMPLE_P1="[Parent1 sample ID]"            # parent1 sample ID, e.g. HG003
_SAMPLE_P2="[Parent2 sample ID]"            # parent2 sample ID, e.g. HG004
_REF=${_INPUT_DIR}/ref.fa                   # change your reference file name here
_OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"          # e.g. ./output
_THREADS="[MAXIMUM_THREADS]"                # e.g. 8
_MODEL_DIR_C3="[Clair3 MODEL NAME]"         # e.g. ./models/clair3_models/ont
_MODEL_DIR_C3T="[Clair3-Trio MODEL NAME]"   # e.g. ./models/clair3_trio_models/c3t_hg002_g422

./run_clair3_trio.sh \
  --bam_fn_c=${_BAM_C} \    
  --bam_fn_p1=${_BAM_P1} \
  --bam_fn_p2=${_BAM_P2} \
  --output=${_OUTPUT_DIR} \
  --ref_fn=${_REF} \
  --threads=${_THREADS} \
  --model_path_clair3="${_MODEL_DIR_C3}" \
  --model_path_clair3_trio="${_MODEL_DIR_C3T}" \
  --sample_name_c=${_SAMPLE_C} \
  --sample_name_p1=${_SAMPLE_P1} \
  --sample_name_p2=${_SAMPLE_P2}

Option 4. Bioconda

# make sure channels are added in conda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

# create conda environment named "clair3-trio"
conda create -n clair3-trio -c bioconda clair3-trio python=3.9.0 -y
conda activate clair3-trio

# run clair3-trio like this afterward
_INPUT_DIR="[YOUR_INPUT_FOLDER]"            # e.g. ./input
_BAM_C=${_INPUT_DIR}/input_child.bam        # chnage your child's bam file name here
_BAM_P1=${_INPUT_DIR}/input_parent1.bam     # chnage your parent-1's bam file name here
_BAM_P2=${_INPUT_DIR}/input_parent2.bam     # chnage your parent-2's bam file name here
_SAMPLE_C="[Child sample ID]"               # child sample ID, e.g. HG002
_SAMPLE_P1="[Parent1 sample ID]"            # parent1 sample ID, e.g. HG003
_SAMPLE_P2="[Parent2 sample ID]"            # parent2 sample ID, e.g. HG004
_REF=${_INPUT_DIR}/ref.fa                   # change your reference file name here
_OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"          # e.g. ./output
_THREADS="[MAXIMUM_THREADS]"                # e.g. 8
_MODEL_DIR_C3="[Clair3 MODEL NAME]"         # e.g. r941_prom_sup_g5014
_MODEL_DIR_C3T="[Clair3-Trio MODEL NAME]"   # e.g. c3t_hg002_r941_prom_sup_g5014

run_clair3_trio.sh \
  --bam_fn_c=${_BAM_C} \    
  --bam_fn_p1=${_BAM_P1} \
  --bam_fn_p2=${_BAM_P2} \
  --output=${_OUTPUT_DIR} \
  --ref_fn=${_REF} \
  --threads=${_THREADS} \
  --model_path_clair3="${CONDA_PREFIX}/bin/models/${_MODEL_DIR_C3}" \ 
  --model_path_clair3_trio="${CONDA_PREFIX}/bin/models/${_MODEL_DIR_C3T}" \ 
  --sample_name_c=${_SAMPLE_C} \
  --sample_name_p1=${_SAMPLE_P1} \
  --sample_name_p2=${_SAMPLE_P2}

Check Usage for more options. Pre-trained models are already included in the bioconda package.

Option 5. Docker Dockerfile

Building a docker image.

# clone Clair3-Trio
git clone https://github.com/hku-bal/Clair3-Trio.git
cd Clair3-Trio

# build a docker image named hkubal/clair3-trio:latest
# might require docker authentication to build docker image 
docker build -f ./Dockerfile -t hkubal/clair3-trio:latest .

# run clair3-trio docker image like 
docker run -it hkubal/clair3-trio:latest /opt/bin/run_clair3_trio.sh --help

Output Files

Clair3-Trio outputs files in VCF/GVCF format for the trio genotype. The output files (for a trio [C ], [P1], [P2]) including:

.
├── run_clair3_trio.log		        # Clair3-Trio running log
├── [C ].vcf.gz				# Called variants in vcf format for [C ]
├── [P1].vcf.gz				# Called variants in vcf format for [P1]
├── [P2].vcf.gz				# Called variants in vcf format for [P2]
├── [C ].gvcf.gz			# Called variants in gvcf format for [C ] (when enabled `--gvcf`)
├── [P1].gvcf.gz			# Called variants in gvcf format for [P2] (when enabled `--gvcf`)
├── [P2].gvcf.gz			# Called variants in gvcf format for [P2] (when enabled `--gvcf`)
├── phased_[C ].vcf.gz			# Called phased variants for [C ] (when enabled `--enable_output_phasing`)		
├── phased_[P1].vcf.gz			# Called phased variants for [P1] (when enabled `--enable_output_phasing`)		
├── phased_[P2].vcf.gz			# Called phased variants for [P2] (when enabled `--enable_output_phasing`)		
├── phased_[C ].bam			# alignment tagged with phased variants info. for [C ] (when enabled `--enable_output_haplotagging`)		
├── phased_[P1].bam			# alignment tagged with phased variants info. for [P1] (when enabled `--enable_output_haplotagging`)		
├── phased_[P2].bam			# alignment tagged with phased variants info. for [P2] (when enabled `--enable_output_haplotagging`)		
├── [C ]_c3t.vcf.gz			# raw variants from Clair-Trio's trio model for [C ]
├── [P1]_c3t.vcf.gz			# raw variants from Clair-Trio's trio model for [P1]
├── [P2]_c3t.vcf.gz			# raw variants from Clair-Trio's trio model for [P2]
├── /log				# folder for detailed running log
└── /tmp				# folder for all running temporary files

Usage

General Usage

Caution: Use =value for optional parameters, e.g. --bed_fn=fn.bed instead of --bed_fn fn.bed.

./run_clair3_trio.sh \
  --bam_fn_c=${_BAM_C} \
  --bam_fn_p1=${_BAM_P1} \
  --bam_fn_p2=${_BAM_P2} \
  --output=${_OUTPUT_DIR} \
  --ref_fn=${_REF} \
  --threads=${_THREADS} \
  --model_path_clair3="${_MODEL_DIR_C3}" \
  --model_path_clair3_trio="${_MODEL_DIR_C3T}" \
  --bed_fn=${_INPUT_DIR}/quick_demo.bed \
  --sample_name_c=${_SAMPLE_C} \
  --sample_name_p1=${_SAMPLE_P1} \
  --sample_name_p2=${_SAMPLE_P2}

Options

Required parameters:

  --bam_fn_c=FILE             	 Child's BAM file input. The input file must be samtools indexed.
  --bam_fn_p1=FILE             	 Parent1's BAM file input (Parent1 can be father or mother). The input file must be samtools indexed.
  --bam_fn_p2=FILE             	 Parent2's BAM file input (Parent2 can be father or mother). The input file must be samtools indexed.
  -f, --ref_fn=FILE              FASTA reference file input. The input file must be samtools indexed.
  --model_path_clair3=STR        The folder path containing a Clair3 model (requiring six files in the folder, including pileup.data-00000-of-00002, pileup.data-00001-of-00002 pileup.index, full_alignment.data-00000-of-00002, full_alignment.data-00001-of-00002  and full_alignment.index.
  --model_path_clair3_trio=STR   The folder path containing a Clair3-Trio model.
  -t, --threads=INT              Max threads to be used. The full genome will be divided into small chunks for parallel processing. Each chunk will use 4 threads. The chunks being processed simultaneously is ceil($threads/4)*3. 3 is the overloading factor.
  -o, --output=PATH              VCF output directory.

Other parameters:

Caution: Use =value for optional parameters, e.g., --bed_fn=fn.bed instead of --bed_fn fn.bed

  --sample_name_c=STR       Define the sample name for Child to be shown in the VCF file.[Child].
  --sample_name_p1=STR      Define the sample name for Parent1 to be shown in the VCF file.[Parent1].
  --sample_name_p2=STR      Define the sample name for Parent2 to be shown in the VCF file.[Parent2].
  --bed_fn=FILE             Call variants only in the provided bed regions.
  --vcf_fn=FILE             Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided.
  --ctg_name=STR            The name of the sequence to be processed.
  --qual=INT                If set, variants with >$qual will be marked PASS, or LowQual otherwise.
  --samtools=STR            Path of samtools, samtools version >= 1.10 is required.
  --python=STR              Path of python, python3 >= 3.6 is required.
  --pypy=STR                Path of pypy3, pypy3 >= 3.6 is required.
  --parallel=STR            Path of parallel, parallel >= 20191122 is required.
  --whatshap=STR            Path of whatshap, whatshap >= 1.0 is required.
  --chunk_size=INT          The size of each chuck for parallel processing, default: 5Mbp.
  --gvcf                    Enable GVCF output, default: disable.
  --print_ref_calls         Show reference calls (0/0) in vcf file, default: disable.
  --include_all_ctgs        Call variants on all contigs, otherwise call in chr{1..22,X,Y} and {1..22,X,Y}, default: disable.
  --snp_min_af=FLOAT        Minimum SNP AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.08.
  --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.

  --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.
  --trio_model_prefix=STR   EXPERIMENTAL: Model prefix in trio calling, including $prefix.data-00000-of-00002, $prefix.data-00001-of-00002 $prefix.index, default: trio.
  --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 Clair3 WhatsHap phasing, default: 0.8 for ont guppy5 and 0.7 for other platforms.
  --enable_output_phasing        Output phased variants using whatshap, default: disable.
  --enable_output_haplotagging   Output enable_output_haplotagging BAM variants using whatshap, default: disable.
  --enable_phasing               It means `--enable_output_phasing`. The option is retained for backward compatibility.

Folder Structure and Submodule Descriptions

Clair3-Trio shares the same folder structure as Clair3, except for an additional folder trio. For descriptions for Clair3 folder, please check Clair3's Descriptions for more inforamtion.

Submodules in clair3/ are for variant calling and model training. Submodules in preprocess are for data preparation.

For all the submodules listed below, you can use -h or --help for available options.

`trio/`	submodules under this folder are pypy incompatible, please run using python
`CheckEnvs_Trio`	Check the environment and validity of the input variables, preprocess the BED input if necessary, `--chunk_size` sets the chuck size to be processed per parallel job.
`SelectCandidates_Trio`	Select trio candidates for clair3-trio calling.
`CallVarBam_Trio`	Call variants using a trained model and three BAM files.
`SortVcf_Trio`	Sort Trio's VCF file.
`MergeTenorsBam_Trio`	Create and merge three tensors into trio's tensors.
`CallVariants_Trio`	Call variants using a trained model and merged tensors of candidate variants.
`model`	define Clair3-Trio model
`Training`	-
`SelectHetSnp_Trio`	Select heterozygous SNP candidates from pileup model and true set.
`Merge_Tenors_Trio`	Merge three tensors into trio's tensors.
`Tensor2Bin_Trio`	Convert trio's tensors into Bin file for training.
`Train_Trio`	Training a trio model using the `RectifiedAdam` optimizer. We also use the `Lookahead` optimizer to adjust the `RectifiedAdam` parameters dynamically. The initial learning rate is `1e-3` with `0.1` learning rate warm-up. Input a binary containing tensors created by `Tensor2Bin_Trio`.
`Evaluation`	-
`Check_de_novo`	Benchmark calling results in terms of de novo variants.

Training Data

Clair3-Trio trained its trio models using four GIAB samples (HG002, HG003 and HG004). All models were trained with chr20 excluded (including only chr1-19, 21, 22). All data links can be found at this page.

Platform	Reference	Aligner	Training samples
ONT	GRCh38_no_alt	minimap2	HG002,3,4

VCF/GVCF Output Formats

Clair3-Trio supports both VCF and GVCF output formats. Clair3-Trio uses VCF version 4.2 specifications. Specifically, Clair3-Trio adds a P INFO tag to the results called using a pileup model, and a T INFO tag to the results called using a trio model.

Clair3-Trio outputs a GATK-compatible GVCF format that passes GATK's ValidateVariants module. Different from DeepVariant that uses <*> to represent any possible alternative allele, Clair3-Trio uses <NON_REF>, the same as GATK.

Clair3-Trio GVCF files can be merged with GLNexus. A GLNexus caller-based configuration file is available Download.

Note that the reference call in VCF is called via Model, and Refcall in GVCF may be inferred from allele depth.

We left some comments for merging multiple VCF/GVCF here.

Publication

Zheng Z, Li S, Su J, Leung AW, Lam TW, Luo R. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Nature Computational Science. 2022 Dec;2(12):797-803.
Su J, Zheng Z, Ahmed SS, Lam TW, Luo R. Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks. Briefings in Bioinformatics. 2022 Sep;23(5):bbac301.

Name		Name	Last commit message	Last commit date
Latest commit History 522 Commits
clair3		clair3
colab		colab
docs		docs
preprocess		preprocess
scripts		scripts
shared		shared
trio		trio
.gitignore		.gitignore
Dockerfile		Dockerfile
LICENSE.md		LICENSE.md
README.md		README.md
__init__.py		__init__.py
clair3.py		clair3.py
run_clair3.sh		run_clair3.sh
run_clair3_trio.sh		run_clair3_trio.sh

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Clair3-Trio: variant calling in trio using Nanopore long-reads

Introduction

Contents

Latest Updates

What's New in Clair3-Trio

Pre-trained Models

Clair3's Pre-trained Models

Quick Demo

Installation

Option 1. Docker pre-built image

Option 2. Singularity

Option 3. Build an anaconda virtual environment

Option 4. Bioconda

Option 5. Docker Dockerfile

Output Files

Usage

General Usage

Options

Folder Structure and Submodule Descriptions

Training Data

VCF/GVCF Output Formats

Publication

About

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Contributors 6

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HKU-BAL/Clair3-Trio

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Repository files navigation

Clair3-Trio: variant calling in trio using Nanopore long-reads

Introduction

Contents

Latest Updates

What's New in Clair3-Trio

Pre-trained Models

Clair3's Pre-trained Models

Quick Demo

Installation

Option 1. Docker pre-built image

Option 2. Singularity

Option 3. Build an anaconda virtual environment

Option 4. Bioconda

Option 5. Docker Dockerfile

Output Files

Usage

General Usage

Options

Folder Structure and Submodule Descriptions

Training Data

VCF/GVCF Output Formats

Publication

About

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Resources

License

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Releases

Contributors 6

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