Uploading VCF Files
VCF (Variant Call Format) files are the primary input for variant analysis in VariantMiner. This guide walks you through the process of uploading VCF files and understanding the automated processing that follows.
Before You Begin
File Requirements
Format: VCF files (.vcf or .vcf.gz)
Compression: Gzipped files (.gz) are recommended for faster uploads
Index files: Tabix index files (.tbi) are optional but recommended
Size limits: Check with your administrator for maximum file sizes
Content: Files should contain variant calls from standard variant callers
Prerequisites
You must have Editor or higher permissions in your workspace
Ensure you have sufficient storage quota available
Have your VCF files ready on your local computer or network
Upload Methods
Method 1: Dashboard Quick Upload
Access the dashboard
Navigate to the main VariantMiner dashboard
Click "Upload New File" button
The Files dashboard showing uploaded VCF files and their processing status
Select your file
Click "Choose File" or drag and drop your VCF file
Select the VCF file from your computer
The file name will appear in the upload field
Configure upload settings
File Name: Edit the display name if desired
Description: Add an optional description
Workspace: Confirm the correct workspace is selected
Start upload
Click "Upload File"
Progress bar will show upload status
Do not close the browser tab during upload
Method 2: Files Section Upload
Navigate to Files
Click "Files" in the main navigation
Select "Upload VCF File" from the files dashboard
File selection
Use the file browser to select your VCF file
Multiple files can be selected for batch upload
Preview file information before uploading
Metadata configuration
Sample Information: Link to existing samples or create new ones
Subject Association: Connect to patient records
File Roles: Specify if this is a primary analysis file or supplementary
Tags: Add searchable tags for organization
Advanced options
Processing Priority: Set processing queue priority
Notification Settings: Configure completion notifications
Storage Options: Choose storage backend (if multiple options available)
Upload Process
During Upload
Progress Tracking: Real-time progress bar shows upload status
Speed Information: Upload speed and estimated time remaining
Cancellation: Option to cancel upload if needed
Error Handling: Automatic retry for network interruptions
Upload Completion
Once upload completes:
File status changes to "Processing"
Background processing begins automatically
Notification sent (if configured)
File appears in your files dashboard
Automated Processing
Processing Pipeline
After upload, VariantMiner automatically:
File Validation
Checks VCF format compliance
Validates headers and sample information
Ensures file integrity
Database Generation
Creates optimized SQLite database for fast querying
Indexes variants for efficient searching
Calculates summary statistics
Annotation Enhancement
Adds additional annotation information
Links to external databases
Calculates pathogenicity scores
Quality Metrics
Generates file quality reports
Calculates variant distribution statistics
Identifies potential issues
Processing Status
Monitor processing through the Files dashboard:
Pending: File uploaded, waiting to start processing
Processing: Active background processing
Completed: Ready for analysis
Error: Processing failed (see error details)
Processing Time
Processing time depends on:
File size: Larger files take longer
Variant count: More variants require more processing time
Server load: Queue position affects start time
Complexity: Multi-sample files take longer
Typical processing times:
Small files (< 100MB): 5-15 minutes
Medium files (100MB - 1GB): 15-60 minutes
Large files (> 1GB): 1-4 hours
File Management After Upload
File Information
Once uploaded, view file details:
File statistics: Variant counts, sample information
Processing logs: Detailed processing information
Quality metrics: File quality assessment
Download options: Access to original and processed files
File Actions
Available actions for uploaded files:
Browse Variants: Open the variant browser
Create Order: Start analysis workflow
Link to Sample: Associate with biological samples
Add to Report: Include variants in clinical reports
Download: Access original or processed files
Delete: Remove file (if permitted)
Troubleshooting Upload Issues
Upload Failures
Slow Upload Speeds
Check your internet connection
Use compressed (.gz) files
Upload during off-peak hours
Contact your network administrator
Upload Interrupted
Resume upload if browser supports it
Clear browser cache and retry
Try a different browser
Check file permissions
File Size Errors
Verify file size limits with administrator
Compress file if not already compressed
Split large files if possible
Check available storage quota
Processing Errors
Format Validation Errors
Verify VCF file format compliance
Check for corrupted headers
Ensure proper sample definitions
Validate with external VCF tools
Processing Timeouts
Very large files may require extended processing time
Contact administrator if processing seems stuck
Check system status and load
Review processing logs for specific errors
Storage Errors
Check workspace storage quota
Verify file system permissions
Contact administrator for storage issues
Clear old files if quota exceeded
Best Practices
File Preparation
Compress files: Use gzip compression for faster uploads
Include index files: Upload .tbi files alongside VCF files
Validate format: Check VCF format before uploading
Plan metadata: Prepare sample and subject information in advance
Organization
Naming conventions: Use consistent, descriptive file names
Descriptions: Add meaningful descriptions for future reference
Tags: Use tags for easy searching and organization
Folder structure: Organize files logically within workspaces
Performance
Upload timing: Upload large files during low-traffic periods
Batch uploads: Group related files for efficient processing
Monitor progress: Watch for errors during upload and processing
Clean up: Remove unnecessary files to maintain performance
Security
Data sensitivity: Ensure files contain appropriate data for the workspace
Access control: Verify workspace permissions before uploading
Compliance: Follow institutional data handling policies
Backup: Maintain backups of original files
Files uploaded successfully? Continue to File Processing Status to learn about monitoring and managing your processed files.
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