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IVA filter reference

Each browser in IVA presents you with a range of filters that you can combine together in queries. You can save these with an alias for future reference/use.

The following is a list of filters available for each browser:

Variant browser

Category Filter Type Description
STUDY AND COHORTS Study Filter Text Filter the variants that are in either both or any of the studies in the same project
Cohort alternate stats Number Retrieve variants founded under the specified (>,<,=) proportion in any of the cohorts defined for the study or any other study in the same project.
GENOMIC Genomic Location Number (chr:position) Filter variants by chromosome/region
Feature IDs Text - autocomplete Filter variants by SNP and Gene IDs
Gene Biotype Pick list with filter Retrieve variants within genes of a precise biotype
Variant Type Pick-list Filter variants of selected type.
Select a preset configuration
Pick-list (Sequence Ontology terms) Filter by preset groups of consequence types (Loss of Function, Protein Truncating, Protein Altering, Coding Sequence, etc.)
Select SO terms
Custom consequence types selection
Pick-list (Sequence Ontology terms) Filter by user-defined consequence types
POPULATION FREQUENCY Select Population Frequency Operator (pick list) and number (text), one for each population study Filter by alternate allele frequency in population studies.
CLINICAL Disease Panels Pick list with filter Filter by genes, genomic locations in pre-configured panels.
ClinVar Accessions Pick list of pathogenicity.
Free text (ClinVar accession)
Filter by ClinVar pathogenicity and/or ClinVar accession number.
Full Text Search on HPO, ClinVAR, protein domains or keywords. Some OMIM and Orphanet IDSs are also supported. Free text Filter by various annotations.
PHENOTYPE GO Accessions Free text (GO accession)
Operator (pick list)
Filter variants by Gene Ontology accessions (max 1000 terms).
HPO Accessions Free text (HPO accession)
Operator (pick list)
Filter variants by Human Phenotype Ontology accessions (max 1000 terms)
DELETERIOUSNESS Protein Substitution Score
* Polyphen
Pick list plus Operator (pick list) and number (text), one for each score (SIFT and Polyphen) SIFT score: Options are either to select a Tolerated/Deleterious qualitative score or to provide a quantitative impact value. SIFT scores <0.05 are considered deleterious.
Polyphen: Options are either a Benign/probably damaging qualitative score or to provide a quantitative impact value. Polyphen scores can be considered Benign (<0.15), Possibly damaging (0.15-0.85) or Damaging (>0.85)
CONSERVATION Conservation Score
* Phylop
* PhastCons
Pick list plus Operator (pick list) and number (text), one for each score Phylop, PhastCons and GERP) PhyloP: measure evolutionary conservation at individual alignment sites; they are useful to evaluate signatures of selection at particular nucleotide or classes of nucleotide (e.g., third codon positions, or first positions of miRNA target sites). Positive scores (max 3.0) mean conserved positions and negative scores (min -14.0) indicate positive selection.
PhastCons estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. Theyrepresent probabilities of negative selection and range between 0 (non-conserved) and 1 (highly conserved).
Genomic Evolutionary Rate Profiling (GERP) estimate the level of conservation of positions. Scores ≥ 2 indicate evolutionary constraint to and ≥ 3 indicate purifying selection.

Catalog browsers

Filter Type Description Sample Individual Family
Sample ID Text Filter by Sample ID Yes Yes Yes
Individual ID Text Filter by the sample from Individual ID Yes Yes Yes
File Name Text file name from which the sample was extracted Yes Yes Yes
Phenotypes Text Retrieve entities for a selected phenotype/s. Yes Yes Yes
Disorders Text Retrieve entities for a selected disorder/s. No Yes Yes
Somatic Boolean Indicates whether the sample comes from a germinal or somatic tissue. Yes No No
Date Date Date when the entity was created. Yes Yes Yes
Annotations Text User-defined annotations for each entity. Yes Yes No