Analysis Nodes

Source Nodes

Provide a source of variants

All Variants

All Variants

All variants in the database.

Cohort

Cohort

A collection of related samples, eg “control group” or “poor responders”

Classifications

Classifications

Pedigree

Pedigree

Variants from family samples filtered by genotype according to inheritance models

Sample

Sample

A sample, usually one genotype (patient, cell or organism) with a set of variants.

Trio

Trio

Mother/Father/Proband - filter for recessive/dominant/denovo inheritance

Filter Nodes

These nodes filter variants connected to the top of them

Built In Filter

Built in Filter

Built in filters used in node counts eg High or Moderate Impact / OMIM / ClinVar Pathological

Damage

Damage

Filter to damage predictions

Filter

Filter

Filter based on column values

Gene List

Gene List

Filter to a list of gene symbols.

../_images/gene_list_node_editor.png

Used Named Gene Lists to select existing Gene Lists. You can select multiple lists at a time.

This node returns variants where ANY TRANSCRIPT matches the genes in the list, see transcript choice

View the “Genes” tab to see which genes are being used by the filter.

Intervals Intersection

Intervals Intersection

Filter based on intersection with genomic ranges (eg .bed files)

Merge

Merge

Merge variants from multiple sources

Phenotype

Phenotype

Filter to gene lists based on ontology keywords

Population

Population

Filter on population frequencies in public databases (gnomAD/Exac/1KG/UK10K) or number of samples in this database.

../_images/population_node_gnomad_population.png

Tags

Tags

Filter variants to those that have been tagged

Tissue Expression

Tissue Expression

Filter based on tissue specific expression (from Human Protein Atlas)

Venn

Venn

A filter based on set intersections between parent nodes

Zygosity

Zygosity

Compound HET and other Zygosity filters