Available filter settings
On the left of the Filter View, the following filters are available and can be customised manually.
Filter set: Use the dropdown menu to select a predefined Filter set to apply to the rare variants in the sample. After selecting a filter set, all individual filters will automatically be set to their corresponding predefined values.
Quality: Use the sliders to change the threshold for overall depth of coverage (DP) and genotype quality (GQ) of variants. Check the box to also show variants with allelic imbalance (threshold for allelic imbalance: alternate allele ratio <0.30 or >0.70).
If DP or GQ fields are missing from (a subset of variants in) the VCF, these will be set at 0 for each variant by default. In order to display variants in the Filter view, these quality filters should hence also be set at 0.
Frequency: Use the sliders or the free input field to adapt frequency thresholds in gnomAD, lab frequency (based on samples in the Moon account) and the Diploid frequency (database of samples on the server). Only those variants that meet all threshold criteria are displayed in the filter view.
When setting the gnomAD slider at 2%, the filter view displays all variants with a gnomAD frequency below 2% in addition to a number of known pathogenic variants with a frequency above 2% in gnomAD.
Both the Lab and Diploid frequency filters can be turned off by setting the sliders at 2%.
Panels: Allows you to select one or more of your labs gene Panels. Filter results show all variants located in genes that are present in at least one of the selected panels. In order to avoid false negative searches, Moon also takes into account synonyms of gene names included in the panel, to perform filtering.
Gene: Type in the name(s) of the gene or genes of interest, separated by a space, to filter variants. Moon takes into account every possible synonym or previous name of a gene based on the entered search. Gene names that are not recognised are highlighted in red. Unrecognised gene names are not taken into account for filtering.
Effect: Specify on or more variant effects to be displayed as a result of filtering. By default, ‘non-synonymous coding' and ‘splicing’ are selected as Effects. A few combination effects are also available for filtering, that already combine some separate variant effects:
Truncating: This filter criterium retains variants with the following effects: stop gained, frameshift, splice site acceptor, splice site donor and start lost/initiator_codon_variant.
Non-synonymous coding: This filter criterium retains variants with the following effects: stop gained, frameshift, splice site acceptor, splice site donor, start lost/initiator_codon_variant, missense, in-frame indel, stop lost.
Splicing: This filter criterium retains splice site acceptor, splice site donor and splice region variants.
Non-coding: this option includes intronic, UTR and non-coding transcript exon variants.
Segregation: The first checkbox allows to only view those variants that segregate with the phenotype in a family analysis based on the ‘healthy’ and ‘affected’ statuses of included family members. The selection menu allows to only visualise variants that are de novo, biparentally inherited, or inherited from one of the parents (paternal/maternal).
SpliceAI: Filters variants based on the annotation of a SpliceAI prediction score with threshold of choice. SpliceAI scores are currently only available for variants in Apollo genes, and within exonic regions or 200 nt flanking intronic sequences. In addition, only 1-2 nt sized indels are automatically annotated.
Zygosity: This filter allows you to select variants of specific zygosity, deduced from the genotype defined in the uploaded VCF.
The “compound heterozygous” option shows true compound heterozygous variants in case both parents are included in the analysis (ie. one variant should be inherited maternally, the second variant paternally), or shows potential compound heterozygous variants, in all other cases.
For X-linked calls in males, both 1/1 and 0/1 calls are considered “hemizygous”.
Disorder: This field allows to enter a disorder name of interest. All variants annotated with an Apollo disorder of which the Apollo disorder name contains the exact searched text, will be displayed. The checkbox below, allows to only display variants for which an Apollo disorder was annotated in the most recent analysis. To only display variants in genes with no disorder annotation, “No associated disorder” can be used as search term in the Disorder search field.
The inheritance filter allows you to select only variants that are annotated with an Apollo disorder with the inheritance pattern of interest. This filter can be combined with the ‘zygosity’ filter to view variants for which there is concordance between genotype and known inheritance (eg. Homozygous variants in genes associated with an autosomal recessive disorder).
Databases: Specify required variant classification(s) in ClinVar or the lab’s Knowledge base, or select certain variant classifications to exclude from the filter results. When selecting multiple classifications in ClinVar and/or the KB, the variants that are displayed should match at least one of the selected classification criteria. Check the box to only view variants that have been reported in scientific literature (based on integration with Mastermind).
Region: Specify a chromosome (eg. “1”, “X”, “MT”), a region within a chromosome (eg.”1:1000-2000”), or an exact chromosomal position (eg. “1:234567) to filter on. If filtering on multiple genomic locations, these should be separated by a semicolon. This works for chromosomes (e.g. X;Y), locations (e.g. 1:4897;1:8965) or genomic ranges (e.g. 1:100-100000;2:100-100000).
Exclusion filter: This field allows you to view variants based on Moon’s reason for their exclusion from the Shortlist (e.g. insufficient phenotype overlap, low quality, gnomAD allele frequency too high, no co-segregation…).