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.
CONSEQUENCE TYPE	Select SO terms 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 * SIFT * 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 * GERP	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