A tool for structural variant (SV) analysis and visualization.
svTyper is a comprehensive tool for analyzing and visualizing structural variants in genomic data. It provides detailed analysis of different types of structural variants including deletions, insertions, duplications, and translocations.
Before installing svTyper, ensure you have the following tools installed:
- Python 3.7 or higher
- R 4.0 or higher
- BWA (Burrows-Wheeler Aligner)
- SAMtools
- BCFtools
- ggplot2
- dplyr
- tidyr
- gridExtra
- pandas
- numpy
- pysam
- click
- tabulate
# Clone the repository
git clone https://github.com/SemiQuant/svTyper.git
# Change to project directory
cd svTyper
# Install Python dependencies
pip install -r requirements.txt
# Install R dependencies
R -e "install.packages(c('ggplot2', 'dplyr', 'tidyr', 'gridExtra'))"svTyper --input input.bam --output results/| Option | Description |
|---|---|
| --input | Input BAM/CRAM/VCF file |
| --output | Output directory |
| --threads | Number of threads to use |
| --verbose | Show detailed progress |
The tool generates:
- Detailed SV analysis reports in tabular format
- Visualization plots for SV distribution
- Quality metrics for detected variants