VAnDa: Variant Annotation Dashboard
Variant annotation server with advanced query builder
Overview
The Advanced Query Builder allows you to create complex filtering conditions on your annotated variant data. It supports logical operators (AND, OR, NOT), parenthetical grouping, and a wide range of comparison operators.
Key Features
- Groups (Parentheses): Group multiple conditions together and evaluate them as a unit
- AND/OR per condition: Each condition has its own logical operator connecting it to the previous condition
- NOT checkbox: Negate any individual condition
- Multiple Groups: Combine groups with AND or OR logic
- All fields available: Filter on any column in your variant data
Getting Started
1. Adding a Condition
Each query starts with a Group containing at least one Condition. A condition consists of:
2. Adding More Conditions
Click to add another condition within the same group. Use the AND/OR dropdown to specify how it connects to the previous condition.
3. Adding Groups (Parentheses)
Click to create a new parenthetical group. When multiple groups exist, use the Groups combined with selector to choose AND or OR between groups.
Operators Reference
| Operator | Symbol | Description | Example |
|---|---|---|---|
contains |
⊃ | Field contains the value (case-insensitive substring match) | SYMBOL contains "BRCA" → matches BRCA1, BRCA2 |
equals |
= | Field exactly matches the value | IMPACT equals "HIGH" |
starts with |
⌃ | Field starts with the value | SYMBOL starts with "BR" |
ends with |
⌄ | Field ends with the value | Consequence ends with "variant" |
> |
> | Numeric greater than | CADD_PHRED > 20 |
< |
< | Numeric less than | gnomADe_AF < 0.01 |
>= |
≥ | Numeric greater than or equal | POS >= 1000000 |
<= |
≤ | Numeric less than or equal | CADD_PHRED <= 15 |
Logic Examples
Example 1: Simple AND
Find HIGH impact variants in the BRCA1 gene:
SYMBOL equals "BRCA1"
AND IMPACT equals "HIGH"
Both conditions must be true for a variant to match.
Example 2: Simple OR
Find variants that are either HIGH impact OR have CADD score > 20:
IMPACT equals "HIGH"
OR CADD_PHRED > 20
Either condition being true is sufficient to match.
Example 3: Using NOT
Find coding variants that are NOT synonymous:
Consequence contains "variant"
AND Consequence equals "synonymous_variant" ☑ NOT
The NOT checkbox inverts the condition.
Example 4: Using Groups (Advanced)
Find (HIGH impact BRCA1/BRCA2 variants) OR (any variant with CADD > 25):
Group 1:
IMPACT equals "HIGH"
AND SYMBOL contains "BRCA"
Group 2:
CADD_PHRED > 25
Group 1 AND Group 2 are combined with OR at the top level.
Available Fields
Variant Identification
CHROM- ChromosomePOS- PositionID- Variant IDREF- Reference alleleALT- Alternate alleleQUAL- Quality scoreFILTER- Filter status
Functional Annotation
Consequence- Variant consequenceIMPACT- Impact level (HIGH/MODERATE/LOW/MODIFIER)SYMBOL- Gene symbolGene- Ensembl Gene ID
Pathogenicity Scores
CADD_PHRED- CADD Phred scorephyloP100way_vertebrate- Conservation score
Population Frequencies
gnomADe_AF- gnomAD exome allele frequencydbNSFP_POPMAX_AF- Maximum population AF
Clinical & Disease
ClinVar_CLNSIG- Clinical significanceClinVar_CLNDISDB- ClinVar disease databaseCancer- Cancer annotation (COSMIC)Cancer_TIER- Cancer tier classificationDisease_description- Disease descriptionOrphanet_disorder- Orphanet disorder nameOrphanet_id- Orphanet ID
Phenotype & HPO
HPO_id- HPO term IDsHPO_name- HPO term namesHPO_Categories- HPO disease categoriesOMIM_id- OMIM IDMIM_disease- MIM disease description