ScanITD
📦 Installation
ScanITD can be installed using Conda (via the Bioconda channel) or pip.
Via Conda (Bioconda)
To install ScanITD using Conda:
conda install -c bioconda scanitd
Or using the modern bioconda::scanitd specifier:
conda install bioconda::scanitd
Via Pip
ScanITD can also be installed using pip, the Python package installer:
-
Ensure you have Python 3.10 or later installed on your system.
-
Create a virtual environment (recommended):
python -m venv scanitd_env source scanitd_env/bin/activate # On Windows use `scanitd_env\Scripts\activate`
-
Install ScanITD:
pip install scanitd
Verification
Verify the installation:
scanitd --help
🛠️ Usage
Usage: scanitd [OPTIONS]
ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation
Required Arguments
-
--input,-iPATH- Aligned BAM file
- Required
-
--ref,-rPATH- Reference genome in FASTA format (with fai index)
- Required
-
--output,-oTEXT- Output VCF file
- Required
Optional Arguments
-
--mapq,-mINTEGER- Minimum MAPQ in BAM for calling ITD
- Default: 15
-
--ao,-cINTEGER- Minimum observation count for ITD
- Default: 4
-
--depth,-dINTEGER- Minimum depth to call ITD
- Default: 10
-
--vaf,-fFLOAT- Minimum variant allele frequency
- Default: 0.1
-
--lengthINTEGER- Minimum ITD length to report
- Default: 10
-
--aln-mismatches,-nINTEGER- Maximum allowed mismatches for pairwise local alignment
- Default: 1
-
--ins-mismatchesINTEGER- Maximum allowed mismatches for insertion-inferred duplication
- Default: 2
-
--target,-tTEXT- 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.
1 maintainer
Metadata
1 maintainer
Release files for scanitd 0.9.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| scanitd-0.9.3.tar.gz | 123.5 kB | With provenance | Details for scanitd-0.9.3.tar.gz |
Built distributions (wheels)
Total release size: 1.1 MB
Release files / scanitd-0.9.3.tar.gz
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