README.md

ScanITD

📦 Installation

ScanITD can be installed using pip, the Python package installer. Follow these steps to install:

1. Ensure you have Python 3.10 or later installed on your system.

2. Create a virtual environment (recommended):

   python -m venv scanitd_env
   source scanitd_env/bin/activate  # On Windows use `scanitd_env\Scripts\activate`

3. Install ScanITD:

   pip install scanitd

4. Verify the installation:

   scanitd --help

🛠️ Usage

Usage: scanitd [OPTIONS]

ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation

Required Arguments

• --input, -i PATH

  • Aligned BAM file
  • Required

• --ref, -r PATH

  • Reference genome in FASTA format (with fai index)
  • Required

• --output, -o TEXT

  • Output VCF file
  • Required

Optional Arguments

• --mapq, -m INTEGER

  • Minimum MAPQ in BAM for calling ITD
  • Default: 15

• --ao, -c INTEGER

  • Minimum observation count for ITD
  • Default: 4

• --depth, -d INTEGER

  • Minimum depth to call ITD
  • Default: 10

• --vaf, -f FLOAT

  • Minimum variant allele frequency
  • Default: 0.1

• --length INTEGER

  • Minimum ITD length to report
  • Default: 10

• --aln-mismatches, -n INTEGER

  • Maximum allowed mismatches for pairwise local alignment
  • Default: 1

• --ins-mismatches INTEGER

  • Maximum allowed mismatches for insertion-inferred duplication
  • Default: 2

• --target, -t TEXT

  • Limit analysis to targets listed in the BED-format file or a samtools region string

• --log-level, -l [info|warning|error|debug|trace]

  • Set the logging level
  • Default: info

• --version, -v

  • Show version and exit

📚 Citation

Wang TY. and Yang R. ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation.