MutationInfo

MutationInfo extracts information from genomic variants as a Python package, retrieving variant position, reference sequence, and alternative sequence while supporting dbSNP rs and HGVS formats.

Key Features:

• Format Support: Processes variants provided in dbSNP rs format and HGVS format.
• get_info method: The get_info method retrieves variant information and accepts method parameters to select extraction approaches.
• Variation Reporter (experimental): method='VARIATION_REPORTER' enables extraction using Variation Reporter.
• TRANSVAR integration: method='TRANSVAR' invokes TRANSVAR-based extraction and requires the TRANSVAR CLI tool to be installed.

Scientific Applications:

• Variant information extraction: Retrieves position, reference allele, and alternative allele for variant annotation and downstream analyses.
• Format interoperability: Supports workflows that require dbSNP rs and HGVS-formatted inputs for genomic analyses.
• External-tool annotation: Enables augmentation of variant data using Variation Reporter and TRANSVAR outputs.

Methodology:

Uses the get_info method with method arguments 'VARIATION_REPORTER' or 'TRANSVAR'; when 'TRANSVAR' is selected, MutationInfo invokes the TRANSVAR CLI; supported input formats include dbSNP rs and HGVS.