From a6613180ed2f35ff24613da9438560d74fcb4d98 Mon Sep 17 00:00:00 2001 From: zhengzhenxian <920596906@qq.com> Date: Mon, 19 Jul 2021 23:07:27 +0800 Subject: [PATCH] update readme --- README.md | 33 ++++++++++++++------------------- 1 file changed, 14 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 1d46cb9..a0bdf60 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,9 @@ 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-r4 (Jun 28)* : 1. Install via [bioconda](#option-3--bioconda). 2. Added an ONT Guppy2 model to the images (`ont_guppy2`). Click [here](docs/guppy2.md) for more benchmarking results. **The results show you have to use the Guppy2 model for Guppy2 or earlier data**. 3. Added [google colab notebooks](colab) for quick demo. 4. Fixed a bug when there are too few variant candidates ([#28](https://github.com/HKU-BAL/Clair3/issues/28)). +*v0.1-r5 (July 19)* : 1. Modified data generator in model training to avoid memory exhaustion and unexpected segmentation fault by Tensorflow (contributor @[ftostevin-ont](https://github.com/ftostevin-ont) ). 2. Simplified dockerfile workflow to reuse container caching (contributor @[amblina](https://github.com/amblina)**). 3. Fixed ALT output for reference calls (contributor @[wdecoster](https://github.com/wdecoster)). 4. Fixed a bug in multi-allelic AF computation (AF of [ACGT]Del variants was wrong before r5). 5. Added AD tag to the GVCF output. 6. Added the `--call_snp_only` option to only call SNP only ([#40](https://github.com/HKU-BAL/Clair3/issues/40)). 7. Added pileup and full-alignment output validity check to avoid workflow crashing ([#32](https://github.com/HKU-BAL/Clair3/issues/32), [#38](https://github.com/HKU-BAL/Clair3/issues/38)). + +*v0.1-r4 (Jun 28)* : 1. Install via [bioconda](https://github.com/HKU-BAL/Clair3#option-3--bioconda). 2. Added an ONT Guppy2 model to the images (`ont_guppy2`). Click [here](https://github.com/HKU-BAL/Clair3/blob/main/docs/guppy2.md) for more benchmarking results. **The results show you have to use the Guppy2 model for Guppy2 or earlier data**. 3. Added [google colab notebooks](https://github.com/HKU-BAL/Clair3/blob/main/colab) for quick demo. 4. Fixed a bug when there are too few variant candidates ([#28](https://github.com/HKU-BAL/Clair3/issues/28)). *v0.1-r3 (Jun 9)* : 1. Added `ulimit -u` (max user processes) check (lowers the `THREADS` if the resource is insufficient) and automatic retries on failed jobs ([#20](https://github.com/HKU-BAL/Clair3/issues/20), [#23](https://github.com/HKU-BAL/Clair3/issues/23), [#24](https://github.com/HKU-BAL/Clair3/issues/24)). 2. Added an ONT Guppy5 model to the images (`ont_guppy5`). Click [here](docs/guppy5.md) for more benchmarks on the Guppy5 model and data. @@ -122,12 +124,11 @@ A pre-built docker image is available [here](https://hub.docker.com/r/hkubal/cla 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-r4" docker run -it \ -v ${INPUT_DIR}:${INPUT_DIR} \ -v ${OUTPUT_DIR}:${OUTPUT_DIR} \ - hkubal/clair3:"${BIN_VERSION}" \ + hkubal/clair3:latest \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here @@ -147,17 +148,16 @@ Check [Usage](#Usage) for more options. INPUT_DIR="[YOUR_INPUT_FOLDER]" # e.g. /home/user1/input (absolute path needed) OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]" # e.g. /home/user1/output (absolute path needed) THREADS="[MAXIMUM_THREADS]" # e.g. 8 -BIN_VERSION="v0.1-r4" conda config --add channels defaults conda create -n singularity-env -c conda-forge singularity -y conda activate singularity-env # singularity pull docker pre-built image -singularity pull docker://hkubal/clair3:v0.1-r4 +singularity pull docker://hkubal/clair3:latest # run clair3 like this afterward -singularity exec clair3_"${BIN_VERSION}".sif \ +singularity exec clair3_latest.sif \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here @@ -255,18 +255,16 @@ tar -zxvf clair3_models.tar.gz -C ./models 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-r4" - # clone Clair3 git clone https://github.com/hku-bal/Clair3.git cd Clair3 -# build a docker image named hkubal/clair3:v0.1-r4 +# build a docker image named hkubal/clair3:latest # might require docker authentication to build docker image -docker build -f ./Dockerfile -t hkubal/clair3:"${BIN_VERSION}" . +docker build -f ./Dockerfile -t hkubal/clair3:latest . # run clair3 docker image like option 1 -docker run -it hkubal/clair3:"${BIN_VERSION}" /opt/bin/run_clair3.sh --help +docker run -it hkubal/clair3:latest /opt/bin/run_clair3.sh --help ``` --- @@ -333,6 +331,7 @@ docker run -it hkubal/clair3:"${BIN_VERSION}" /opt/bin/run_clair3.sh --help --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. --no_phasing_for_fa EXPERIMENTAL: Call variants without whatshap phasing in full alignment calling, default: disable. + --call_snp_only EXPERIMENTAL: Call candidates pass SNP minimum AF only, ignore Indel candidates, default: disable. ``` #### Call variants in a chromosome @@ -342,12 +341,11 @@ CONTIGS_LIST="[YOUR_CONTIGS_LIST]" # e.g "chr21" or "chr21,chr22" 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-r4" docker run -it \ -v ${INPUT_DIR}:${INPUT_DIR} \ -v ${OUTPUT_DIR}:${OUTPUT_DIR} \ - hkubal/clair3:"${BIN_VERSION}" \ + hkubal/clair3:latest \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here @@ -365,12 +363,11 @@ KNOWN_VARIANTS_VCF="[YOUR_VCF_PATH]" # e.g. /home/user1/known_variants.vcf.gz 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-r4" docker run -it \ -v ${INPUT_DIR}:${INPUT_DIR} \ -v ${OUTPUT_DIR}:${OUTPUT_DIR} \ - hkubal/clair3:"${BIN_VERSION}" \ + hkubal/clair3:latest \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here @@ -400,12 +397,11 @@ BED_FILE_PATH="[YOUR_BED_FILE]" # e.g. /home/user1/tmp.bed (absolute path 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-r4" docker run -it \ -v ${INPUT_DIR}:${INPUT_DIR} \ -v ${OUTPUT_DIR}:${OUTPUT_DIR} \ - hkubal/clair3:"${BIN_VERSION}" \ + hkubal/clair3:latest \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here @@ -422,12 +418,11 @@ docker run -it \ 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-r4" docker run -it \ -v ${INPUT_DIR}:${INPUT_DIR} \ -v ${OUTPUT_DIR}:${OUTPUT_DIR} \ - hkubal/clair3:"${BIN_VERSION}" \ + hkubal/clair3:latest \ /opt/bin/run_clair3.sh \ --bam_fn=${INPUT_DIR}/input.bam \ ## change your bam file name here --ref_fn=${INPUT_DIR}/ref.fa \ ## change your reference file name here