Independently developed free software for downloading authorized BAM, BAI, and VCF files from the varvis® API for research and bioinformatics workflow automation.
# Set credentials (recommended)
export VARVIS_USER="your_username"
export VARVIS_PASSWORD="your_password"
# Download BAM files for specific analyses
./varvis-download.js -t mytarget -a "12345,67890" -f "bam,bam.bai"
# Download with genomic range filtering
./varvis-download.js -t mytarget -a 12345 -g "chr1:1000000-2000000"
# List available files without downloading
./varvis-download.js -t mytarget -a 12345 --listgit clone https://github.com/LaborBerlin/varvis-download.git
cd varvis-download
npm install
chmod +x varvis-download.js
npm link # Optional: global installationFind files by analysis IDs, sample IDs, or LIMS IDs with powerful filtering expressions.
Support for BAM, BAI, VCF, and VCF.GZ files with automatic index handling.
Extract specific genomic regions using coordinates or BED files for focused research data retrieval.
Provided for research, educational, development, interoperability, and bioinformatics workflow automation purposes only. Review the Intended Use page before using the software in regulated environments.
Seamless handling of archived files with restoration requests and automated workflows.
Detailed download reports, metrics tracking, and configurable logging levels.
Proxy configuration, batch processing, and CI/CD integration capabilities.