vcf-stats-viz 0.1.1

Herramienta para el análisis y visualización de variantes genómicas (VCF) con visualizacion interactiva.

vcf-stats-viz

vcf-stats-viz is a command-line tool for efficient analysis of VCF (Variant Call Format) files and for generating an interactive local web dashboard for variant exploration.

The package is designed to handle large-scale VCF files with a strong emphasis on low memory usage. It achieves this through chunk-based processing, avoiding loading the entire file into memory. Analysis results are stored on disk and can be reused without reprocessing the original VCF file.

Key features

• Memory-efficient processing of large VCF files using chunk-based parsing
• Generation of variant statistics and summary datasets
• Persistent storage of analysis results and metadata
• Local web-based dashboard for interactive visualization and filtering of variants
• Support for multiple stored analyses
• Simple and reproducible command-line interface

Installation

pip install vcf-stats-viz

The package installs the following command-line entry point:

vcf-analyze

Basic usage

Run a complete analysis of a VCF file and launch the local web dashboard:

vcf-analyze input.vcf

By default, the dashboard is available at:

http://127.0.0.1:5000

Common options

Limit the number of processed variants:

vcf-analyze input.vcf 100000

Adjust the chunk size used during processing:

vcf-analyze input.vcf --chunk-size 50000

Run the analysis without launching the web dashboard:

vcf-analyze input.vcf --no-dashboard

Launch the web dashboard using previously generated results:

vcf-analyze --dashboard-only

Use cases

• Exploratory analysis of genomic variants
• Preliminary processing of large VCF datasets
• Local visualization of variant statistics without external services
• Validation and debugging of bioinformatics pipelines

Console entry point

The package exposes the following console script:

vcf-analyze = "vcf_stats.main:main"

License

This project is licensed under the MIT License.