Frequently Asked Questions

After your imputation service is complete, you can download your imputed files:

1. Log in to your account
2. Navigate to the "Products" section
3. Look for your imputed file (it will be listed as a separate sample)
4. Click on the sample to view details
5. Click the "Download" button to get your imputed RAW file

What is an imputed file?
The imputation service extends your DNA file from approximately 700,000 SNPs to over 30 million SNPs using advanced statistical algorithms and reference populations. This provides more comprehensive genetic data for analysis.

File Details:

• Format: Standard RAW format compatible with most analysis tools
• Size: Significantly larger than your original file (100MB+)
• Processing time: Available within 24-72 hours after payment

Your phased files are available in the Products section after processing:

1. Log in to your account
2. Go to "Products" in the main menu
3. Find your phased file sample
4. Click to view details and download options
5. Download your phased RAW file

What is a phased file?
Phasing determines which DNA variants (alleles) you inherited from your mother vs. your father. This is useful for:

• Understanding parental genetic contributions
• More accurate ancestry analysis
• Genealogy research and matching
• Advanced genetic studies

Phasing Options:

• Single Phasing: Statistical phasing without parental data
• Duo/Trio Phasing: Uses parent(s) DNA for highly accurate phasing

Processing time: 24-48 hours after order placement.

DNA imputation is an advanced service that dramatically expands your genetic data:

What is Imputation?

Imputation uses statistical algorithms and large reference populations to predict ("impute") genetic markers that weren't directly tested by your DNA company.

• Your original file: ~600,000 - 700,000 SNPs
• After imputation: 30+ million SNPs
• Increase: 40-50x more genetic information!

Why You Need Imputation:

• Enhanced Analysis: Access to reports requiring more markers
• Better Accuracy: More data points = more precise results
• Compatibility: Work with tools requiring high-density data
• Research: Participate in studies needing comprehensive data
• Medical Insights: Analyze health markers not on consumer chips
• Rare Variants: Discover less common genetic variations

How It Works:

1. Upload your standard DNA file
2. Purchase imputation service
3. Our algorithms compare your data to reference populations
4. Statistical models predict missing SNPs with high accuracy
5. Receive expanded file in 24-72 hours

What You Get:

• Extended RAW file with 30+ million SNPs
• Compatible with all our reports and tools
• Downloadable for use on other platforms
• Significantly improved analysis capabilities

Accuracy:

• Imputation accuracy: 95-99% depending on ancestry
• Based on large reference panels (1000 Genomes, HapMap, etc.)
• Best for European, Asian, African ancestries
• Works with all standard consumer DNA files

Included in Explorer Pack:

The imputation service is included with our Explorer Pack, along with numerous reports and tools.

DNA phasing is a process that determines which genetic variants you inherited from your mother versus your father:

Understanding Phasing:

Humans have two copies of each chromosome - one from each parent. Standard DNA files show you have specific variants, but don't indicate which parent contributed which allele. Phasing solves this problem.

Example:

• Unphased data: "You have A and G at position rs1234567"
• Phased data: "You inherited A from your mother and G from your father"

Why Phasing Matters:

• Genealogy: Trace specific DNA segments to maternal/paternal ancestors
• Ancestry: More accurate ethnic composition analysis
• Matching: Better DNA relative matching
• Health: Understand inherited conditions from specific parents
• Research: Essential for advanced genetic studies

Types of Phasing:

1. Statistical (Single) Phasing:

• Uses algorithms and reference populations
• Works with just your DNA file
• 85-95% accurate
• Good for general ancestry analysis

2. Duo/Trio Phasing:

• Uses parent(s) DNA files along with yours
• Direct comparison determines inheritance
• 99%+ accurate
• Best for detailed genealogy work
• Requires DNA files from one or both parents

How to Phase Your DNA:

1. Purchase phasing service from our store
2. Upload your DNA file (for single phasing)
3. Or upload your file + parent files (for duo/trio phasing)
4. Receive phased file in 24-48 hours

Phased File Uses:

• Upload to genealogy sites for better matching
• Use in advanced ancestry calculators
• Research and academic studies
• Preserve phased data for family members

DNA phasing affects heterozygous and homozygous SNPs differently:

Heterozygous SNPs:

These are positions where you have two different alleles (variants).

Before Phasing:

• You know you have A and G
• Unknown which came from which parent
• Represented as: AG or GA (unordered)

After Phasing:

• Maternal chromosome: A
• Paternal chromosome: G
• Clear parental assignment

Impact: Phasing is MOST useful for heterozygous SNPs because it resolves parental inheritance.

Homozygous SNPs:

These are positions where you have two identical alleles.

Before and After Phasing:

• Both chromosomes: A-A or G-G
• Phasing doesn't change anything
• Both alleles from same parent aren't distinguishable
• You inherited the same variant from both parents

Impact: Phasing has NO practical effect on homozygous SNPs since both copies are identical.

Why This Matters:

• Ancestry Analysis: Heterozygous SNPs reveal which parent contributed which ancestry
• DNA Matching: Helps identify which DNA segments match specific relatives
• Genetic Studies: Important for understanding compound heterozygosity
• Chromosome Mapping: Enables accurate chromosome painting

SNP Distribution:

In a typical human genome:

• ~3-4 million heterozygous SNPs (phasing helps here)
• ~1-2 million homozygous SNPs (phasing doesn't matter)

If your DNA file has already been phased, there's generally no need to phase it again:

When Files Are Already Phased:

• Your file already contains parental chromosome information
• Each SNP is assigned to maternal or paternal chromosome
• The data is complete for phasing purposes

However, You CAN Perform Additional Analyses:

1. Identify Variations:

• Look for specific mutations or variants
• Analyze rare genetic markers
• Study disease-associated SNPs

2. Comparative Analysis:

• Compare to reference genomes
• Identify differences from population averages
• Study ancestry-specific variations

3. Inheritance Predictions:

• Predict traits passed to offspring
• Calculate recombination probabilities
• Estimate genetic contribution to children

4. Re-phasing Considerations:

You might want to re-phase if:

• Better method available: Newer algorithms with improved accuracy
• Additional data: Parent DNA files now available for trio phasing
• Quality concerns: Original phasing had low quality scores
• Different reference panel: Using population-specific references

Phasing Quality:

The accuracy of phased data depends on:

• Quality and coverage of original data
• Phasing method used (statistical vs. trio)
• Reference populations in phasing algorithm
• Ancestry background (common ancestries phase better)

Our Recommendation:

If your file is already well-phased (especially from trio phasing), additional phasing provides minimal benefit. Focus instead on analysis and interpretation of the phased data.

Yes! DNA analysis can reconstruct approximately half of each parent's DNA from your genetic data:

How It Works:

You inherit exactly 50% of your DNA from each parent. Using your DNA file, we can identify and separate:

• Genetic variants inherited from your mother
• Genetic variants inherited from your father
• Specific chromosome segments from each parent

What You Need:

Best Case - Trio Phasing:

• Your DNA file
• Your mother's DNA file
• Your father's DNA file
• Result: Highly accurate (99%+) parental reconstruction

Good Case - Duo Phasing:

• Your DNA file
• One parent's DNA file
• Result: Very accurate reconstruction of inherited segments

Basic Case - Statistical Phasing:

• Only your DNA file
• Uses population reference data
• Result: 85-95% accurate estimation

Applications:

• Genealogy: Trace ancestry to specific grandparents
• Medical: Identify which parent passed health-related variants
• Ancestry Analysis: Separate maternal/paternal ethnic origins
• DNA Matching: Determine relation through specific parent
• Family Research: Reconstruct deceased parent's genetic profile

What Can Be Reconstructed:

• Specific SNPs from each parent
• Chromosome segments and their parental origin
• Ethnic composition by parent
• Haplogroups (direct maternal and paternal lineages)

Limitations:

• Can only reconstruct the 50% you inherited
• The other 50% each parent has is not in your DNA
• Siblings have different combinations (except identical twins)
• Accuracy depends on method and data quality

How to Get Started:

Purchase our Phasing Service (Single or Duo/Trio) from the store to begin parental DNA reconstruction.

Our imputation service provides high accuracy for expanding your genetic data:

Overall Accuracy:

• General accuracy range: 95-99%
• Common variants: 98-99% accurate
• Less common variants: 90-95% accurate
• Rare variants: 85-90% accurate

Factors Affecting Accuracy:

1. Ancestry Background:

2. Reference Populations:

• We use comprehensive reference panels:
• 1000 Genomes Project
• HapMap databases
• Population-specific references
• Latest genetic research data

3. Original File Quality:

• High-quality chips (Illumina GSA): Best accuracy
• Older chips: Slightly lower accuracy
• More SNPs in original file: Better imputation

What Accuracy Means:

• 95% accuracy = 95 out of 100 imputed SNPs are correct
• For 30 million imputed SNPs, 28.5-29.7 million are accurate
• Common variants (found in many people) are most accurate
• Rare variants have more uncertainty

Quality Scores:

• Each imputed SNP includes a quality/confidence score
• High-confidence SNPs can be trusted like genotyped SNPs
• Low-confidence SNPs are flagged for careful interpretation

Scientific Validation:

• Our methods based on peer-reviewed research
• Continuously validated against new data
• Regularly updated with improved algorithms
• Comparable to academic and clinical imputation

Use Cases:

• Ancestry analysis: High accuracy for admixture and ethnicity
• Trait predictions: Reliable for most common traits
• Research: Suitable for population studies
• Exploration: Excellent for genetic discovery

Note: Imputation is a prediction, not direct testing. For critical medical decisions, direct genotyping or sequencing is recommended.

Phasing services differ in accuracy and data requirements:

Single (Statistical) Phasing:

What it uses:

• Only your DNA file
• Statistical algorithms
• Large reference populations
• Population linkage patterns

How it works:

• Analyzes patterns in your DNA
• Compares to known haplotype blocks
• Predicts most likely parental assignments
• Uses probability models

Accuracy: 85-95%

Best for:

• When parent DNA is unavailable
• General ancestry analysis
• Basic genealogy work
• Budget-friendly option

Duo Phasing:

What it uses:

• Your DNA file
• ONE parent's DNA file
• Direct comparison

How it works:

• Directly compares your DNA to parent's DNA
• Identifies which variants came from that parent
• Infers remaining variants came from other parent
• Minimal statistical guessing

Accuracy: 97-99%

Best for:

• One parent available for testing
• Deceased or unavailable parent
• High-accuracy needs

Trio Phasing:

What it uses:

• Your DNA file
• Mother's DNA file
• Father's DNA file
• Complete direct comparison

How it works:

• Direct comparison to both parents
• Identifies exact inheritance from each
• Nearly eliminates statistical uncertainty
• Gold standard for phasing

Accuracy: 99%+

Best for:

• Both parents available
• Maximum accuracy needed
• Research or medical purposes
• Genealogy preservation

Comparison Table:

Which Should You Choose?

• Single: Parents unavailable, general use
• Duo: One parent available, good balance
• Trio: Both parents available, best results

DNA annotation services add valuable context and information to your genetic data:

What is Annotation?

Annotation means adding biological and medical information to each genetic variant in your DNA file, explaining what each SNP means and its potential effects.

What Gets Added:

• Gene information: Which gene the SNP is in or near
• Functional effects: Impact on protein function
• Clinical significance: Known disease associations
• Population frequencies: How common the variant is
• Literature references: Published research about the SNP
• Databases: Links to dbSNP, ClinVar, OMIM

Key Benefits:

1. Medical Insights:

• Identify medically relevant variants
• Understand health risk factors
• Find pharmacogenetic markers (drug response)
• Discover carrier status for genetic conditions

2. Research Ready:

• Prepare files for genetic research
• Compatible with analysis software
• Scientific publication-ready
• Standardized formats (VEP, SnpEff compatible)

3. Better Understanding:

• Learn what your DNA variants mean
• Understand genetic mechanisms
• Connect variants to traits
• Educational value

4. Clinical Applications:

• Share with healthcare providers
• Genetic counseling support
• Personalized medicine
• Disease risk assessment

5. Advanced Analysis:

• Filter variants by medical relevance
• Prioritize important SNPs
• Pathway analysis
• Gene set enrichment

Annotation Services We Offer:

VCF Annotation:

• Add comprehensive annotations to VCF files
• Include allele frequencies
• Functional predictions
• Clinical interpretations

RAW File Annotation:

• Annotate standard RAW DNA files
• Add gene context
• Include trait associations
• Export in various formats

Use Cases:

• Medical professionals: Clinical interpretation
• Researchers: Scientific studies
• Genealogists: Understanding inheritance
• Enthusiasts: Deep genetic exploration
• Educators: Teaching genetics

Output Formats:

• Annotated VCF files
• Spreadsheet-compatible formats
• JSON for programming
• Human-readable reports

Annotation transforms raw genetic data into meaningful, actionable information.

Our WGS (Whole Genome Sequencing) to RAW conversion service transforms your comprehensive genome data into a universally compatible format:

What is WGS?

• WGS sequences your entire genome (all 3 billion+ base pairs)
• Provides comprehensive genetic information
• More detailed than SNP chip testing (which tests 600K-700K positions)
• Files are typically in BAM, CRAM, or VCF format
• File sizes: 50GB-200GB+ (too large for most platforms)

What is a RAW File?

• Standard format used by consumer DNA companies
• Contains positions relevant for ancestry and traits
• Compatible with 23andMe, AncestryDNA, MyHeritage, FTDNA
• File size: 10-50MB (much more manageable)
• Easy to upload and analyze

Conversion Process:

1. Upload/Submit: Provide your WGS file (via secure link)
2. Extraction: We extract relevant SNP positions
3. Format Conversion: Transform to standard RAW format
4. Quality Control: Verify data integrity
5. Haplogroup Analysis: Determine MTDNA and YDNA lineages
6. Delivery: Receive RAW file + haplogroup report
7. Timeframe: 12-48 hours

What You Receive:

• RAW DNA File: In 23andMe or AncestryDNA format
• MTDNA Haplogroup: Maternal lineage
• YDNA Haplogroup: Paternal lineage (for males)
• Quality Report: Data quality metrics
• SNP Count: Number of positions extracted

Key Benefits:

• Universal Compatibility: Works with all ancestry sites
• Manageable Size: From 100GB+ to 20MB
• Preserves Quality: Maintains WGS accuracy
• Multiple Uses: Upload to many platforms
• Family Sharing: Easy to share with relatives

Compatible WGS Providers:

• Nebula Genomics
• Dante Labs
• YSEQ
• Full Genomes Corporation
• Sequencing.com
• Any provider offering BAM/CRAM/VCF files

Supported Input Formats:

• BAM: Binary Alignment Map
• CRAM: Compressed Reference-oriented Alignment Map
• VCF: Variant Call Format (WGS-derived)
• FASTQ: Raw sequencing reads (slower processing)

Use Your Converted File:

• Upload to DNA Genics for all our reports
• Upload to GEDmatch for DNA matching
• Upload to MyHeritage, FTDNA for family matching
• Use in third-party analysis tools
• Share with genetic counselors

Note: This service is specifically for WGS BAM/CRAM files. For smaller VCF files, use our "VCF to RAW" service instead.

Yes, but there are important considerations about VCF to RAW conversion:

Valid Use Cases:

1. Platform Compatibility:

• Converting WGS-derived VCF to use on ancestry sites
• Making data compatible with 23andMe, AncestryDNA formats
• Enabling upload to genealogy platforms
• Using with third-party analysis tools

2. Data Management:

• Reducing file size for easier handling
• Standardizing format across family members
• Creating backups in different formats
• Sharing with relatives in accessible format

3. Analysis Tools:

• Using tools that require RAW format
• Running calculators expecting consumer DNA format
• Third-party ancestry analysis
• Trait prediction tools

Important Limitations:

VCF Files Have Restrictions:

• Variant-Only: VCF files typically only include variations, not all positions
• Coverage Varies: May not have all SNPs needed for some analysis
• Quality Dependent: Accuracy depends on original sequencing quality
• Not All Equal: WGS VCF ≠ SNP array VCF

Special Considerations:

For WGS-Derived VCF Files:

• Excellent source material
• High quality and comprehensive
• RAW conversion works very well
• Recommended for ancestry use

For SNP Array VCF Files:

• May have limited usefulness
• Already in restricted format
• Conversion may not add value
• Check original source

NOT Recommended For:

• MyHeritage/FTDNA/LivingDNA Compatibility: These platforms work best with WGS to RAW service
• Medical Decision Making: VCF conversions should not replace direct testing
• Clinical Diagnosis: Use proper clinical testing instead
• Low-Quality VCF: Poor input = poor output

Our Service:

Our VCF to RAW service is designed for:

• Individuals with WGS tests (Nebula, Dante, YSEQ)
• Those needing file conversion for analysis tools
• Research and educational purposes
• Genealogy applications

However, we strongly recommend:

• If you have BAM/CRAM files, use "WGS to RAW" service instead
• WGS to RAW provides better quality and compatibility
• VCF to RAW is a secondary option when BAM/CRAM unavailable

Before Converting:

• Verify your VCF file origin and quality
• Understand what data it contains
• Consider if conversion will meet your needs
• Check if original BAM/CRAM files are available

For questions about whether VCF to RAW conversion is right for your specific case, contact our support team.