From 36ca868c3208f08bd48ab93a5d6e593fc24ad520 Mon Sep 17 00:00:00 2001 From: zhengzhenxian <920596906@qq.com> Date: Wed, 19 May 2021 12:31:18 +0800 Subject: [PATCH] update readme --- README.md | 92 ++++++++++++++++++--------------- docs/full_alignment_training.md | 6 +-- docs/pileup_training.md | 4 +- run_clair3.sh | 47 ++++++++--------- 4 files changed, 78 insertions(+), 71 deletions(-) diff --git a/README.md b/README.md index 2f7cc20..d2eacec 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Clair3 is the 3rd generation of [Clair](https://github.com/HKU-BAL/Cl We are actively fixing bugs and issues in Clair3 reported by users. -*v0.1-r1 (May 18)* : 1. Support relative path in Singularity and Conda, Docker still requires absolute path ([#5](https://github.com/HKU-BAL/Clair3/issues/5)). 2. Fix `taskset` CPU-core visibility and provide a Singularity image ([#6](https://github.com/HKU-BAL/Clair3/issues/6)). +*v0.1-r1 (May 18)* : 1. Support relative path in Conda, but Docker and Singularity still requires absolute path ([#5](https://github.com/HKU-BAL/Clair3/issues/5)). 2. Fix `taskset` CPU-core visibility and provide a Singularity image ([#6](https://github.com/HKU-BAL/Clair3/issues/6)). *v0.1 (May 17)*: Initial release. @@ -93,11 +93,11 @@ Check the results using `less ${HOME}/clair3_ont_quickDemo/output/merge_output.v A pre-built docker image is available [here](https://hub.docker.com/layers/hkubal/clair3/latest/images/sha256-769a241a9e1aab422d7309022ab14e8982d1e2af32c24ee7c16230c24b52cd74?context=explore). With it you can run Clair3 using a single command. -**Caution**: Absolute path is needed for both INPUT_DIR and OUTPUT_DIR. +**Caution**: Absolute path is needed for both `INPUT_DIR` and `OUTPUT_DIR`. ```bash -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input (absolute path needed) -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output (absolute path needed) +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" @@ -118,9 +118,11 @@ Check [Usage](#Usage) for more options. ### Option 2. Singularity +**Caution**: Absolute path is needed for both `INPUT_DIR` and `OUTPUT_DIR`. + ```bash -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" @@ -159,8 +161,8 @@ chmod +x ./Miniconda3-latest-Linux-x86_64.sh *For using Clair3 on Illumina data, after the following steps, please also install the* [Boost Graph Library](https://www.boost.org/doc/libs/1_65_1/libs/graph/doc/index.html) *using this* [guidance](docs/quick_demo/illumina_quick_demo.md#step-2-install-boost-graph-library-for-illumina-realignment-process). ```bash -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ./input +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ./output THREADS="[MAXIMUM_THREADS]" # e.g. 8 # create and activate an environment named clair3 @@ -202,6 +204,8 @@ tar -zxvf clair3_models.tar.gz -C ./models ### Option 4. Docker Dockerfile +This is the same as option 1 except that you are building a docker image yourself. Please refer to option 1 for usage. + ```bash BIN_VERSION="v0.1-r1" @@ -223,16 +227,16 @@ docker run -it hkubal/clair3:"${BIN_VERSION}" /opt/bin/run_clair3.sh --help ### General Usage +**Caution**: Use `=value` for optional parameters, e.g. `--bed_fn=fn.bed` instead of `--bed_fn fn.bed`. + ```bash -# optional parameters should use "=" ./run_clair3.sh \ --bam_fn=${BAM} \ --ref_fn=${REF} \ --threads=${THREADS} \ - --platform='ont' \ ## options: {ont,hifi,ilmn} + --platform="ont" \ ## options: {ont,hifi,ilmn} --model_path=${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: ${OUTPUT_DIR}/merge_output.vcf.gz @@ -243,36 +247,38 @@ docker run -it hkubal/clair3:"${BIN_VERSION}" /opt/bin/run_clair3.sh --help **Required parameters:** ```bash - -b, --bam_fn FILE BAM file input. The input file must be samtools indexed. - -f, --ref_fn FILE FASTA reference file input. The input file must be samtools indexed. - -m, --model_path STR The folder path containing a Clair3 model (requiring six files in the folder, including pileup.data-00000-of-00001, pileup.index, pileup.meta, full_alignment.data-00000-of-00001, full_alignment.index, and full_alignment.meta). - -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($threads/4)*3. 3 is the overloading factor. - -p, --platform STR Select the sequencing platform of the input. Possible options: {ont,hifi,ilmn}. - -o, --output PATH VCF/GVCF output directory. + -b, --bam_fn=FILE BAM file input. The input file must be samtools indexed. + -f, --ref_fn=FILE FASTA reference file input. The input file must be samtools indexed. + -m, --model_path=STR The folder path containing a Clair3 model (requiring six files in the folder, including pileup.data-00000-of-00001, pileup.index, pileup.meta, full_alignment.data-00000-of-00001, full_alignment.index, and full_alignment.meta). + -t, --threads=INT Max threads to be used. The full genome will be divided into small chunks for parallel processing. Each chunk will use 4 threads. The chunks being processed simultaneously is ceil($threads/4)*3. 3 is the overloading factor. + -p, --platform=STR Select the sequencing platform of the input. Possible options: {ont,hifi,ilmn}. + -o, --output=PATH VCF/GVCF output directory. ``` **Other parameters:** + **Caution**: Use `=value` for optional parameters, e.g., `--bed_fn=fn.bed` instead of `--bed_fn fn.bed` + ```bash - --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. - --sample_name STR Define the sample name to be shown in the VCF file. - --qual INT If set, variants with >=$qual will be marked PASS, or LowQual otherwise. - --samtools STR Path of samtools, samtools version >= 1.10 is required. - --python STR Path of python, python3 >= 3.6 is required. - --pypy STR Path of pypy3, pypy3 >= 3.6 is required. - --parallel STR Path of parallel, parallel >= 20191122 is required. - --whatshap STR Path of whatshap, whatshap >= 1.0 is required. - --chunk_size INT The size of each chuck for parallel processing, default: 5Mbp. + --bed_fn=FILE Call variants only in the provided bed regions. + --vcf_fn=FILE Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided. + --ctg_name=STR The name of the sequence to be processed. + --sample_name=STR Define the sample name to be shown in the VCF file. + --qual=INT If set, variants with >=$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. --pileup_only Use the pileup model only when calling, 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. --gvcf Enable GVCF output, 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,hifi:0.08,ilmn: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,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. + --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,hifi:0.08,ilmn: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,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. --fast_mode EXPERIMENTAL: Skip variant candidates with AF <= 0.15, default: disable. --haploid_precise EXPERIMENTAL: Enable haploid calling mode. Only 1/1 is considered as a variant, default: disable. --haploid_sensitive EXPERIMENTAL: Enable haploid calling mode. 0/1 and 1/1 are considered as a variant, default: disable. @@ -283,8 +289,8 @@ docker run -it hkubal/clair3:"${BIN_VERSION}" /opt/bin/run_clair3.sh --help ```bash CONTIGS_LIST="[YOUR_CONTIGS_LIST]" # e.g "chr21" or "chr21,chr22" -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" @@ -305,9 +311,9 @@ docker run -it \ #### Call variants at known variant sites ```bash -KNOWN_VARIANTS_VCF="[YOUR_VCF_PATH]" # e.g. ~/known_variants.vcf.gz -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +KNOWN_VARIANTS_VCF="[YOUR_VCF_PATH]" # e.g. /home/user1/known_variants.vcf.gz (absolute path needed) +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" @@ -334,15 +340,15 @@ We highly recommended using BED file to define the regions of interest like: CONTIGS="[YOUR_CONTIGS_NAME]" # e.g. chr22 START_POS="[YOUR_START_POS]" # e.g. 0 END_POS="[YOUR_END_POS]" # e.g 10000 -echo -e "${CONTIGS}\t${START_POS}\t${END_POS}" > tmp.bed +echo -e "${CONTIGS}\t${START_POS}\t${END_POS}" > /home/user1/tmp.bed ## change directory accordingly ``` Then run Clair3 like this: ```bash -BED_FILE_PATH=tmp.bed -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +BED_FILE_PATH="[YOUR_BED_FILE]" # e.g. /home/user1/tmp.bed (absolute path needed) +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" @@ -363,8 +369,8 @@ docker run -it \ #### Call variants in non-diploid organisms (Haploid calling) ```bash -INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. ~/input -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. ~/output +INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 BIN_VERSION="v0.1-r1" diff --git a/docs/full_alignment_training.md b/docs/full_alignment_training.md index 6697dee..29a68d7 100644 --- a/docs/full_alignment_training.md +++ b/docs/full_alignment_training.md @@ -56,7 +56,7 @@ PLATFORM="[SEQUENCING_PLATFORM]" # e.g. {ont, hifi, ilmn} VCF_FILE_PATH="[YOUR_VCF_FILE_PATH]" # e.g. hg003.vcf.gz BAM_FILE_PATH="[YOUR_BAM_FILE_PATH]" # e.g. hg003.bam REFERENCE_FILE_PATH="[YOUR_FASTA_FILE_PATH]" # e.g. hg003.fasta -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output # Temporary working directories PHASE_VCF_PATH="${OUTPUT_DIR}/phased_vcf" @@ -145,7 +145,7 @@ This section shows how to build multiple compressed tensor binary file for multi ```bash # Setup executable variables -CLAIR3="clair3.py" # clair3.py +CLAIR3="clair3.py" # clair3.py PYPY="[PYPY_BIN_PATH]" # e.g. pypy3 PYTHON3="[PYTHON3_BIN_PATH]" # e.g. python3 PARALLEL="[PARALLEL_BIN_PATH]" # e.g. parallel @@ -159,7 +159,7 @@ DEPTHS="[YOUR_DEPTHS_OF_SAMPLES_ARRAY]" # e.g. 1000 (means no ALL_REFERENCE_FILE_PATH="[YOUR_FASTA_FILE_PATH_ARRAY]" # e.g. hg002.fasta ALL_BED_FILE_PATH="[YOUR_BED_FILE_PATH_ARRAY]" # e.g. hg002.bed ALL_SAMPLE="[YOUR_SAMPLE_NAME_ARRAY]" # e.g. hg002 -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output_folder +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output_folder # Each line represent one input BAM with a matched coverage in the "DEPTH" array ## check the "Training data subsamping" section on how to apply BAM subsampling diff --git a/docs/pileup_training.md b/docs/pileup_training.md index dbb6c43..eb719a4 100644 --- a/docs/pileup_training.md +++ b/docs/pileup_training.md @@ -94,7 +94,7 @@ This section shows how to build multiple compressed tensor binary files for mult #### 1. Setup variables ```bash # Setup executable variables -CLAIR3="clair3.py" # clair3.py +CLAIR3="clair3.py" # clair3.py PYPY="[PYPY_BIN_PATH]" # e.g. pypy3 PYTHON3="[PYTHON3_BIN_PATH]" # e.g. python3 PARALLEL="[PARALLEL_BIN_PATH]" # e.g. parallel @@ -108,7 +108,7 @@ DEPTHS="[YOUR_DEPTHS_OF_SAMPLES_ARRAY]" # e.g. 1000 (means no s ALL_REFERENCE_FILE_PATH="[YOUR_FASTA_FILE_PATH_ARRAY]" # e.g. hg002.fasta ALL_BED_FILE_PATH="[YOUR_BED_FILE_PATH_ARRAY]" # e.g. hg002.bed ALL_SAMPLE="[YOUR_SAMPLE_NAME_ARRAY]" # e.g. hg002 -OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output_folder +OUTPUT_DIR="[YOUR_OUTPUT_FOLDER_PATH]" # e.g. output_folder # Each line represent one input BAM with a matched coverage in the "DEPTH" array ## check the "Training data subsamping" section on how to apply BAM subsampling diff --git a/run_clair3.sh b/run_clair3.sh index e7be8b0..783794b 100755 --- a/run_clair3.sh +++ b/run_clair3.sh @@ -1,7 +1,7 @@ #!/bin/bash SCRIPT_NAME=$(basename "$0") SCRIPT_PATH=`dirname "$0"` -Usage="Usage: ./${SCRIPT_NAME} -b BAM -f REF -o OUTPUT_DIR -t THREADS -p PLATFORM -m MODEL_PREFIX [--bed_fn=BED] [options]" +Usage="Usage: ./${SCRIPT_NAME} --bam_fn=BAM --ref_fn=REF --output=OUTPUT_DIR --threads=THREADS --platform=PLATFORM --model_path=MODEL_PREFIX [--bed_fn=BED] [options]" set -e #./run_clair3.sh -b tmp.bam -f ref.fasta -t 32 -o tmp -p ont -m model_path @@ -11,33 +11,34 @@ print_help_messages() echo ${Usage} echo $'' echo $'Required parameters:' - echo $' -b, --bam_fn FILE BAM file input. The input file must be samtools indexed.' - echo $' -f, --ref_fn FILE FASTA reference file input. The input file must be samtools indexed.' - echo $' -m, --model_path STR The folder path containing a Clair3 model (requiring six files in the folder, including pileup.data-00000-of-00001, pileup.index, pileup.meta, full_alignment.data-00000-of-00001, full_alignment.index, and full_alignment.meta).' - echo $' -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.' - echo $' -p, --platform STR Select the sequencing platform of the input. Possible options: {ont,hifi,ilmn}.' - echo $' -o, --output PATH VCF/GVCF output directory.' + echo $' -b, --bam_fn=FILE BAM file input. The input file must be samtools indexed.' + echo $' -f, --ref_fn=FILE FASTA reference file input. The input file must be samtools indexed.' + echo $' -m, --model_path=STR The folder path containing a Clair3 model (requiring six files in the folder, including pileup.data-00000-of-00001, pileup.index, pileup.meta, full_alignment.data-00000-of-00001, full_alignment.index, and full_alignment.meta).' + echo $' -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.' + echo $' -p, --platform=STR Select the sequencing platform of the input. Possible options: {ont,hifi,ilmn}.' + echo $' -o, --output=PATH VCF/GVCF output directory.' echo $'' - echo $'Optional parameters:' - echo $' --bed_fn FILE Call variants only in the provided bed regions.' - echo $' --vcf_fn FILE Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided.' - echo $' --ctg_name STR The name of the sequence to be processed.' - echo $' --sample_name STR Define the sample name to be shown in the VCF file.' - echo $' --qual INT If set, variants with >=$qual will be marked PASS, or LowQual otherwise.' - echo $' --samtools STR Path of samtools, samtools version >= 1.10 is required.' - echo $' --python STR Path of python, python3 >= 3.6 is required.' - echo $' --pypy STR Path of pypy3, pypy3 >= 3.6 is required.' - echo $' --parallel STR Path of parallel, parallel >= 20191122 is required.' - echo $' --whatshap STR Path of whatshap, whatshap >= 1.0 is required.' - echo $' --chunk_size INT The size of each chuck for parallel processing, default: 5Mbp.' + echo $'' + echo $"Optional parameters (Use \"=value\" instead of \" value\". E.g., \"--bed_fn=fn.bed\" instead of \"--bed_fn fn.bed\".):" + echo $' --bed_fn=FILE Call variants only in the provided bed regions.' + echo $' --vcf_fn=FILE Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided.' + echo $' --ctg_name=STR The name of the sequence to be processed.' + echo $' --sample_name=STR Define the sample name to be shown in the VCF file.' + echo $' --qual=INT If set, variants with >=$qual will be marked PASS, or LowQual otherwise.' + echo $' --samtools=STR Path of samtools, samtools version >= 1.10 is required.' + echo $' --python=STR Path of python, python3 >= 3.6 is required.' + echo $' --pypy=STR Path of pypy3, pypy3 >= 3.6 is required.' + echo $' --parallel=STR Path of parallel, parallel >= 20191122 is required.' + echo $' --whatshap=STR Path of whatshap, whatshap >= 1.0 is required.' + echo $' --chunk_size=INT The size of each chuck for parallel processing, default: 5Mbp.' echo $' --pileup_only Use the pileup model only when calling, default: disable.' echo $' --print_ref_calls Show reference calls (0/0) in VCF file, default: disable.' echo $' --include_all_ctgs Call variants on all contigs, otherwise call in chr{1..22,X,Y} and {1..22,X,Y}, default: disable.' echo $' --gvcf Enable GVCF output, default: disable.' - echo $' --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,hifi:0.08,ilmn:0.08.' - echo $' --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.' - echo $' --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.' - echo $' --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.' + echo $' --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,hifi:0.08,ilmn:0.08.' + echo $' --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.' + echo $' --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.' + echo $' --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.' echo $' --fast_mode EXPERIMENTAL: Skip variant candidates with AF <= 0.15, default: disable.' echo $' --haploid_precise EXPERIMENTAL: Enable haploid calling mode. Only 1/1 is considered as a variant, default: disable.' echo $' --haploid_sensitive EXPERIMENTAL: Enable haploid calling mode. 0/1 and 1/1 are considered as a variant, default: disable.'