The PhenoDist pipeline is built for generating phenotype distributions for alleles in variant positions and utilizing statistical methods to test for variant position significance.
In order to run the PhenoDist pipeline, users need to install Miniconda and prepare the Miniconda environment in their computing systems.
The required software, programming languages, and packages include:
bwa>=0.7.17
gatk4>=4.4.0.0
samtools>=1.6
htslib>=1.3
python>=3.12
snakemake>=8.4
scipy>=1.12
numpy>=1.26
pandas>=2.2
Beagle>=5.2
SnpEff>=4.3
Miniconda can be downloaded from https://docs.anaconda.com/free/miniconda/.
For example, if users plan to install Miniconda3 Linux 64-bit, the wget tool can be used to download the Miniconda.
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
To install Miniconda in a server or cluster, users can use the command below.
Please remember to replace the <installation_shell_script> with the actual Miniconda installation shell script. In our case, it is Miniconda3-latest-Linux-x86_64.sh.
Please also remember to replace the <desired_new_directory> with an actual directory absolute path.
chmod 777 -R <installation_shell_script>
./<installation_shell_script> -b -u -p <desired_new_directory>
rm -rf <installation_shell_script>
After installing Miniconda, initialization of Miniconda for bash shell can be done using the command below.
Please also remember to replace the <desired_new_directory> with an actual directory absolute path.
<desired_new_directory>/bin/conda init bash
Installation of the Miniconda is required, and Miniconda environment needs to be activated every time before running the PhenoDist pipeline.
Write a Conda configuration file (.condarc) before creating a Conda environment:
nano ~/.condarc
Put the following text into the Conda configuration file (make sure you change envs_dirs and pkgs_dirs) then save the file.
Please make sure not use tab in this yaml file, use 4 spaces instead.
Please make sure to replace /new/path/to/ with an actual directory absolute path.
envs_dirs:
- /new/path/to/miniconda/envs
pkgs_dirs:
- /new/path/to/miniconda/pkgs
channels:
- conda-forge
- bioconda
- defaults
Create a Conda environment by specifying all required packages (option 1).
Please make sure to replace the <conda_environment_name> with an environment name of your choice.
conda create -n <conda_environment_name> bioconda::gatk4 bioconda::samtools bioconda::bcftools bioconda::htslib \
bioconda::bedtools bioconda::bwa bioconda::snakemake bioconda::snakemake-executor-plugin-cluster-generic \
conda-forge::numpy conda-forge::pandas conda-forge::scipy
Create a Conda environment by using a yaml environment file (option 2).
Please make sure to replace the <conda_environment_name> with an environment name of your choice.
conda create --name <conda_environment_name> --file PhenoDist-environment.yml
Create a Conda environment by using a explicit specification file (option 3).
Please make sure to replace the <conda_environment_name> with an environment name of your choice.
conda create --name <conda_environment_name> --file PhenoDist-spec-file.txt
Activate Conda environment using conda activate command.
This step is required every time before running PhenoDist pipeline.
Please make sure to replace the <conda_environment_name> with an environment name of your choice.
conda activate <conda_environment_name>
You can install the PhenoDist from Github with:
git clone https://github.com/yenon118/PhenoDist.git
Create a "tools" folder within the PhenoDist pipeline clone.
cd PhenoDist
mkdir -p tools
cd tools
The Beagle imputation tool can be downloaded from https://faculty.washington.edu/browning/beagle/beagle.html and placed inside the "tools" folder.
The SnpEff functional effect prediction tool can be downloaded from https://pcingola.github.io/SnpEff/download/ and placed in the "tools" folder.
Please save the file with .json extension.
{
"project_name": "Test_Soy1066",
"workflow_path": "/storage/htc/joshilab/yenc/projects/PhenoDist",
"input_files": [
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr01.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr02.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr03.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr04.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr05.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr06.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr07.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr08.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr09.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr10.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr11.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr12.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr13.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr14.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr15.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr16.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr17.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr18.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr19.vcf.gz",
"/storage/htc/joshilab/yenc/projects/PhenoDist/data/test_Soy1066/unimpute_data/test_Soy1066_Chr20.vcf.gz"
],
"chromosomes": [
"Chr01",
"Chr02",
"Chr03",
"Chr04",
"Chr05",
"Chr06",
"Chr07",
"Chr08",
"Chr09",
"Chr10",
"Chr11",
"Chr12",
"Chr13",
"Chr14",
"Chr15",
"Chr16",
"Chr17",
"Chr18",
"Chr19",
"Chr20"
],
"beagle_window": 40,
"genome_version": "Wm82.a2.v1",
"accession_mapping_file": "/storage/htc/joshilab/yenc/projects/PhenoDist/data/act_Soy2939_Accession_Mapping.tsv",
"accession_key": "Accession",
"phenotype_key": "GRIN_Accession",
"phenotype_file": "/storage/htc/joshilab/yenc/projects/PhenoDist/data/act_Soy2939_Phenotype_Data.tsv",
"phenotypes": [
"HEIGHT",
"PODCOLOR"
],
"output_folder": "/storage/htc/joshilab/yenc/projects/PhenoDist/output/Test_Soy1066/",
"memory": 100,
"threads": 4
}
snakemake -j NUMBER_OF_JOBS --configfile CONFIGURATION_FILE --snakefile SNAKEMAKE_FILE
Mandatory Positional Argumants:
NUMBER_OF_JOBS - the number of jobs
CONFIGURATION_FILE - a configuration file
SNAKEMAKE_FILE - the PhenoDist.smk file that sit inside this repository
Below are some fundamental examples illustrating the usage of the PhenoDist pipeline.
Please adjust /path/to/ to an actual directory absolute path.
Examples of running without an executor.
cd /path/to/PhenoDist
snakemake -pj 3 --configfile lewis_slurm_inputs.json --snakefile PhenoDist.smk
Examples of running with an executor.
Snakemake version >= 8.0.0.
cd /path/to/PhenoDist
snakemake --executor cluster-generic \
--cluster-generic-submit-cmd "sbatch --account=xulab --time=0-02:00 \
--nodes=1 --ntasks=1 --cpus-per-task=3 \
--partition=Lewis,BioCompute,hpc5,General --mem=64G" \
--jobs 25 --latency-wait 60 \
--configfile lewis_slurm_inputs.json \
--snakefile PhenoDist.smk
Snakemake version < 8.0.0.
cd /path/to/PhenoDist
snakemake --cluster "sbatch --account=xulab --time=0-02:00 \
--nodes=1 --ntasks=1 --cpus-per-task=3 \
--partition=Lewis,BioCompute,hpc5,General --mem=64G" \
--jobs 25 --latency-wait 60 \
--configfile lewis_slurm_inputs.json \
--snakefile PhenoDist.smk
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