Alamut Parser

This repository provides a script to convert Alamut .mut XML files or .db SQLite files to VCF or TSV formats, consolidating all mutations into a single output file. The script supports coordinate conversion to GRCh38 and includes flexible output options.

Features

• Converts Alamut .mut XML files or .db SQLite files to VCF, TSV, or managed_variants (Scout-compatible) formats
• Supports coordinate systems: GRCh36, GRCh37 (hg19), GRCh38, and LRG
• Converts all coordinates to GRCh38 using chain files and LRG BED files
• Includes rich INFO/column fields in output (pathogenicity, classification, comments, etc.)
• Optionally includes or omits the 'chr' prefix in chromosome names

Requirements

• Python 3.7+
• pyliftover
• pyfaidx
• beautifulsoup4

Install dependencies with:

Usage

python alamut-parser.py \
    -i <input_dir_or_db> \
    -o <output_file> \
    -d <chain_files_dir> \
    -f <format> [options]

Arguments

• -i, --input Input directory with .mut files or path to .db SQLite file
• -o, --outfile Output file path
• -d, --chain-files-dir Directory with chain files and LRG mapping files
• -f, --format Output format: vcf, tsv, or managed_variants

Options

• --include-comments Include comments in output
• --fasta Path to target genome FASTA file (for sequence context)
• --target-genome Target genome assembly (default: GRCh38)
• --institute Institute name (for managed_variants)
• --cancer Specify if cancer variants (for managed_variants)
• --chr-prefix Include 'chr' prefix in chromosome names
• -v, --verbose Enable verbose logging

Example

python alamut-parser.py \
    -i ./mut_files/ \
    -o output.vcf \
    -d ./chainfiles/ \
    -f vcf --include-comments --chr-prefix

Notes

• Chain files and LRG BED files must be present in the specified directory.
• For managed_variants output, the file is compatible with Scout.

License

MIT