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Need two separate virtual environment for the input generation and the evaluation of AIVariant due to the confiliting packages and the version requirements!!!
AIVariant input generation environment
conda create {input environment name}
conda activate {input environment name}
conda install python=3.6.9 numpy -c condaforge
conda install samtools=1.9 -c bioconda
pip install pysam==0.11.2.2 pyBigWig==0.3.17 liftover==1.1.14
AIVariant evaluation environment
conda create {evaluation environment name}
conda activate {evaluation environment name}
# Follow the instruction in https://www.tensorflow.org/ to install tensorflow >= 2.9
git clone https://github.com/Genome4me/AIVariant.git
You should also download the necessary epigenetic data files:
#Run the following commands inside the git cloned directory
wget https://www.encodeproject.org/files/ENCFF338EDE/@@download/ENCFF338EDE.bigWig -O ./AIVariant/bin/encode/pvals/H3K9me3_HepG2.bigWig
wget https://www.encodeproject.org/files/ENCFF881LOL/@@download/ENCFF881LOL.bigWig -O ./AIVariant/bin/encode/folds/H3K9me3_HepG2.bigWig
Before running the provided shell script, CONDA_PREFIX environment variable should be set to base conda path:
>$CONDA_PREFIX
above should return ~/anaconda3 or ~/miniconda, if not then set the environment variable.
Example usage:
#Run the following commands inside the git cloned directory
cd AIVariant
bash run.sh -i {input environment name} -e {evaluation environment name} -t {tumor BAM file path} -n {normal BAM file path} -r {reference FASTA file path} -g {hg19 or hg38 depends on the reference} -o {output directory path} -d {estimated depth of input bam files}
or if you have multiple gpus and want to specify the gpu id:
#Run the following commands inside the git cloned directory
cd AIVariant
CUDA_VISIBLE_DEVICES={gpu id} bash run.sh -i {input environment name} -e {evaluation environment name} -t {tumor BAM file path} -n {normal BAM file path} -r {reference FASTA file path} -g {hg19 or hg38 depends on the reference} -o {output directory path} -d {estimated depth of input bam files}
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