mutator is a pipeline for variant calling and analysis of mitochondrial DNA from ATAC-seq data.
Before using mutator, ensure you have the following prerequisites installed: Miniconda (Python v3.6 or higher): Miniconda Installation Guide (https://docs.conda.io/en/latest/miniconda.html)
Clone the mutator repository:
git clone https://github.com/mik2044/mutator
Create and activate a new conda environment (This environment should be active whenever you are installing dependencies or running the pipeline):
conda create -n [environment]
conda activate [environment]
Install the following dependencies within the conda environment:
- VEP (https://anaconda.org/bioconda/ensembl-vep, version 95.3 recommended)
- cutadapt (https://anaconda.org/bioconda/cutadapt)
- vt (https://anaconda.org/bioconda/vt)
- vcf2maf (https://anaconda.org/bioconda/vcf2maf)
- samtools (https://anaconda.org/bioconda/samtools)
- biopython (https://anaconda.org/conda-forge/biopython)
conda install -c bioconda ensembl-vep=95.3
conda install -c bioconda vt
conda install -c bioconda cutadapt
conda install -c bioconda pysam
conda install -c bioconda bwa
conda install -c bioconda vcf2maf
conda install gatk4=4.4.0.0
conda install -c conda-forge biopython
conda install numpy
conda install pandas
To run the mutator pipeline, use the following command:
python3 mutator.py -s [sample_id] -r [reference] -d [workingdir]
sample_id: Path to the sample. This can either be a full path or just the sample ID if the current directory contains the sample.
reference: Path to the reference fasta file.
workingdir: Path to directory containing the mutator.py file.