IVA filter reference¶
Each browser in IVA present the user with a range of filters used to construct queries. As a result, queries can combine any number of filters.
Filters can be saved with an user-defined alias for future reference/use.
The following is a list of filters available for each browser.
|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 (
||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
|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)
|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.
|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|