Order Creation Wizard
The Order Creation Wizard is a step-by-step guided process for setting up analysis orders in VariantMiner. This wizard simplifies the complex task of configuring genomic analyses by breaking it down into manageable steps.
When to Use the Order Creation Wizard
The wizard is ideal for:
New users learning the platform
Complex analyses involving multiple samples
Family studies requiring proband designation
Quality control to ensure proper configuration
Standardized workflows following institutional protocols
Starting the Wizard
Access Methods
From Dashboard:
Click "Create Order" on the main dashboard
Select "Use Wizard" option
From Orders Section:
Navigate to Orders in the main menu
Click "New Order" button
Choose "Guided Wizard"
From Files:
Browse to processed VCF files
Click "Create Order" next to any file
Wizard opens with file pre-selected
Step 1: Select VCF Files
File Selection
The wizard begins by helping you choose the VCF files for analysis:
Step 1 of the Order Creation Wizard showing VCF file selection
Available Files: List shows all processed VCF files in your workspace
File Status: Only files with "Completed" processing status are available
File Information: View file details including sample count and processing date
Multiple Selection: Choose multiple files for multi-sample analysis
File Requirements
Files must be fully processed (green status indicator)
VCF files should contain the samples you want to analyze
Index files (.tbi) should be present for optimal performance
File Actions
Preview: Click file name to preview variant counts and samples
Details: View detailed file information and quality metrics
Filter: Search files by name, date, or tags
Example Selection:
✅ Patient_001_germline.vcf.gz (Processed: 2024-01-15, 45,231 variants)
✅ Patient_002_tumor.vcf.gz (Processed: 2024-01-15, 67,892 variants)
❌ Patient_003_normal.vcf.gz (Processing: 78% complete)Step 2: Monitor File Processing
Real-Time Status
If selected files are still processing, this step shows:
Real-time file processing status with progress indicators
Processing Progress: Individual file progress bars
Estimated Completion: Time remaining for each file
Queue Position: Current position in processing queue
Auto-Refresh: Page updates automatically with status changes
Processing Details
Current Stage: What processing step is running
Variant Count: Running count of variants processed
Quality Metrics: Real-time quality assessment
Error Handling: Alerts for any processing issues
Wait or Continue Options
Wait for Completion: Stay on this step until all files finish
Continue Later: Save wizard progress and return when files are ready
Select Different Files: Go back and choose already-processed files
Step 3: Configure Samples
Sample Detection
The wizard automatically detects samples from selected VCF files:
Sample Names: Extracted from VCF headers
File Source: Shows which file contains each sample
Duplicate Detection: Identifies samples present in multiple files
Sample Configuration
For each detected sample, configure:
Sample Information:
Display Name: Human-readable sample name
Sample Type: Tumor, Normal, Germline, etc.
Description: Optional detailed description
Collection Date: When the sample was collected
Subject Association:
Link to Existing Subject: Choose from your subjects list
Create New Subject: Set up a new patient record
Subject Details: Patient ID, demographics, clinical information
File Roles:
Primary Analysis: Main file for this sample
Supplementary: Additional files (CNV, SV, etc.)
Quality Control: QC-specific files
Family Relationships
For family studies:
Proband Designation: Mark the primary affected individual
Family Members: Link related samples
Inheritance Patterns: Specify expected inheritance
Parental Information: Link parent-child relationships
Example Configuration:
Sample: PROBAND_001
├── Subject: Patient John Doe (ID: P001)
├── Type: Germline
├── Role: Primary Analysis
└── Family: Proband (affected)
Sample: MOTHER_001
├── Subject: Patient Jane Doe (ID: P002)
├── Type: Germline
├── Role: Primary Analysis
└── Family: Mother (unaffected)Step 4: Analysis Settings
Analysis Type
Choose the type of analysis to perform:
Germline Analysis: Constitutional variants
Somatic Analysis: Tumor-specific variants
Family Analysis: Inheritance patterns and segregation
Comparative Analysis: Tumor vs. normal comparison
Quality Filters
Configure variant quality filters:
Quality Score Threshold: Minimum variant quality
Coverage Depth: Minimum read depth
Allele Frequency: Population frequency filters
Genotype Quality: Minimum genotype quality scores
Annotation Options
Select annotation databases and tools:
Clinical Databases: ClinVar, HGMD, OMIM
Population Databases: gnomAD, 1000 Genomes
Prediction Tools: SIFT, PolyPhen, CADD
Pathway Databases: KEGG, Reactome
Custom Parameters
Advanced users can configure:
Custom Filters: Additional filtering criteria
Processing Options: Memory and CPU allocations
Output Formats: Additional export formats
Notification Settings: Analysis completion alerts
Step 5: Review and Confirm
Order Summary
Review all configuration before submission:
Final review step showing order summary before submission
Files and Samples:
List of selected VCF files
Sample configurations and subject associations
Family relationships and proband designation
Analysis Parameters:
Analysis type and quality filters
Selected annotation databases
Custom parameters and settings
Metadata:
Order name and description
Priority level and estimated completion time
Notification recipients
Validation Checks
The wizard performs final validation:
Required Fields: Ensures all mandatory information is provided
Data Consistency: Checks for conflicts or missing data
Resource Availability: Confirms sufficient computational resources
Permission Verification: Validates user permissions for all operations
Order Submission
Once validation passes:
Review Summary: Final chance to review configuration
Submit Order: Click "Create Order" to submit
Confirmation: Receive order ID and tracking information
Automatic Redirect: Navigate to order monitoring page
Wizard Features
Progress Tracking
Step Indicators: Visual progress through wizard steps
Breadcrumb Navigation: Easy navigation between completed steps
Save and Resume: Save progress and return later
Step Validation: Each step validates before allowing progress
Help and Guidance
Contextual Help: Help text and tooltips on each step
Field Descriptions: Detailed explanations for configuration options
Best Practices: Recommended settings for common use cases
Example Configurations: Pre-configured templates for standard analyses
Error Handling
Validation Messages: Clear error messages with correction guidance
Field Highlighting: Visual indicators for required or error fields
Auto-Save: Automatic saving of wizard progress
Recovery Options: Ability to recover from errors and continue
Advanced Wizard Options
Template-Based Creation
Saved Templates: Reuse previous order configurations
Institutional Templates: Pre-configured analysis types
Template Sharing: Share configurations between users
Template Management: Create, edit, and delete templates
Batch Order Creation
Multiple Probands: Create orders for multiple unrelated samples
Study Cohorts: Set up analysis for research cohorts
Quality Control Batches: Batch QC analysis orders
Automated Splitting: Automatically split large cohorts
Integration Features
LIMS Integration: Import sample information from laboratory systems
External Databases: Query external databases for subject information
API Access: Programmatic order creation for automated workflows
Notification Systems: Integration with institutional notification systems
Tips for Effective Use
Preparation
Plan Analysis: Decide on analysis type and parameters before starting
Organize Files: Ensure VCF files are properly processed and organized
Subject Information: Have patient/subject information readily available
Review Templates: Check for existing templates that match your needs
Best Practices
Descriptive Names: Use clear, descriptive names for orders and samples
Consistent Metadata: Follow institutional naming conventions
Quality Standards: Use appropriate quality filters for your analysis type
Documentation: Add detailed descriptions for future reference
Troubleshooting
Incomplete Files: Ensure all VCF files are fully processed before starting
Permission Errors: Verify workspace permissions for all operations
Missing Subjects: Create subject records before associating samples
Configuration Conflicts: Review error messages and adjust settings
Order created successfully? Continue to Order Management to learn about monitoring and managing your analysis orders.
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