Genotype Browser Section

The configuration section for a genotype browser follows the general INI format. Its name must be genotypeBrowser - this will indicate that it is a genotype browser configuration section. This configuration section must properly describe the genotype browser for the study. This is an optional section.

Example Configuration

[genotypeBrowser]
hasCNV = no
hasComplex = no
hasStudyTypes = no
hasStudyFilters = no
hasFamilyFilters = yes
hasPresentInRole = no
hasPresentInChild = no
hasPresentInParent = no
hasPedigreeSelector = yes
hasGraphicalPreview = yes
inheritanceTypeFilter = mendelian, denovo
selectedInheritanceTypeFilterValues = mendelian, denovo

selectedPhenoFiltersValues = continuous

phenoFilters.continuous.name = Continuous
phenoFilters.continuous.measureType = continuous
phenoFilters.continuous.filter = multi:prb

selectedPresentInRoleValues = parent

presentInRole.parent.name = Parents
presentInRole.parent.roles = mom,dad

selectedGenotypeColumnValues = family,variant,inchild

genotype.family.name = family
genotype.family.slots = family:family id,studyName:study

genotype.variant.name = variant
genotype.variant.slots = location:location,variant:variant

genotype.genotype.name = genotype
genotype.genotype.source = pedigree
genotype.genotype.slots = inChild:in child,fromParent:from parent

genotype.inchild.name = in child
genotype.inchild.source = inChS

genotype.fromparent.name = from parent
genotype.fromparent.source = fromParentS

selectedPhenoColumnValues = pheno

pheno.pheno.name = Measures
pheno.pheno.slots = prb:i1.age:Age:%%.2f,
    prb:i1.iq:Iq:%%.2f

selectedInRolesValues = inChild,fromParentS

inRoles.inChild.destination = inChS
inRoles.inChild.roles = prb,sib

inRoles.fromParents.destination = fromParentS
inRoles.fromParents.roles = mom,dad

previewColumns = family,variant,pheno
downloadColumns = family,variant,inchild

Columns

genotypeBrowser section support different types of columns. These columns are:

  • Genotype - Here you can define columns from the raw study data columns. Configuration of this columns can be found here.

  • Phenotype - Here you can define columns from phenoDB by the id of the phenotype measure. Configuration of this columns can be found here.

  • In Roles - Here you can define columns which are based on the pedigree information. They will be added to the variant as new genotype columns. Information that this columns will be containing will be all possible combinations of the role from all of the defined roles list in it with the gender of the people with this role. Configuration of this columns can be found here. This columns can be used as a genotype columns.

  • Gene Weights - Here you can define columns which are based on the Gene Weights data. They will be added to the variant as new genotype columns. This columns can be used as a genotype columns.

Only Genotype and Phenotype columns can be used as a Preview and Download columns.

Here you can see example configuration for different column types:

[genotypeBrowser]

...

# Genotype columns
#############################################################################

genotype.family.name = family
genotype.family.slots = family:family id,studyName:study

genotype.variant.name = variant
genotype.variant.slots = location:location,variant:variant

genotype.genotype.name = genotype
genotype.genotype.source = pedigree
genotype.genotype.slots = inChS:in child,fromParentS:from parent

# Phenotype columns
#############################################################################

pheno.iq.name = Proband IQs
pheno.iq.slots = prb:diagnosis_summary.best_nonverbal_iq:NvIQ,
    prb:diagnosis_summary.best_verbal_iq:vIQ

# In Roles columns
#############################################################################

inRoles.inChild.destination = inChS
inRoles.inChild.roles = prb,sib

inRoles.fromParents.destination = fromParentS
inRoles.fromParents.roles = mom,dad

genotype.inchild.name = in child
genotype.inchild.source = inChS

genotype.fromparent.name = from parent
genotype.fromparent.source = fromParentS

# Gene Weights columns
#############################################################################

genotype.weights.name = vulnerability/intolerance
genotype.weights.slots = LGD_rank:LGD rank:LGD %%d ,
    RVIS_rank:RVIS rank:RVIS %%d,pLI_rank:pLI rank:pLI %%d

# Preview and Download columns
#############################################################################

previewColumns = family,variant,genotype,weights
downloadColumns=family,variant,fromparent,inchild,weights,iq

...

[genotypeBrowser]

The properties for this section are explained below.

hasCNV

hasCNV = <boolean>

This property determines:

  • if the CNV+ and CNV* effect types (part of the CNV effect group) are present in the Effect Types filter in the Genotype Browser for the study.

  • if the CNV, CNV+ and CNV* effect types are present in the Effect Types filter in the Phenotype Tool for the study.

  • if the CNV variant type is present in the Variant Types filter in the Genotype Browser for the study.

This property takes a boolean value.

hasComplex

hasComplex = <boolean>

This property determines whether the complex variant type is present in the Variant Types filter in the Genotype Browser for the study. This property takes a boolean value.

hasStudyTypes

hasStudyTypes = <boolean>

This property determines whether the Study Types filter is present in the Genotype Browser for the study. This property takes a boolean value.

hasStudyFilters

hasStudyFilters = <boolean>

This property determines whether the Studies filter block is present in the Genotype Browser for the study. This property takes a boolean value.

hasFamilyFilters

hasFamilyFilters = <boolean>

This property determines if the Family filter block is present in the Genotype Browser and Phenotype Tool for the study. This property takes a boolean value.

hasPresentInRole

hasPresentInRole = <boolean>

This property determines if the Present in Role filter is present in the Genotype Browser for the study. This property takes a boolean value. You can see the configuration of Present in Role here.

hasPresentInChild

hasPresentInChild = <boolean>

This property determines if the Present in Child filter is present in the Genotype Browser for the study. This property takes a boolean value.

hasPresentInParent

hasPresentInParent = <boolean>

This property determines if the Present in Parent filter is present in the Genotype Browser for the study. This property takes a boolean value.

hasPedigreeSelector

hasPedigreeSelector = <boolean>

This property determines if the Pedigree Selector filter is present in the Genotype Browser for the study. This property takes a boolean value. The Pedigree Selector filter presents the configured people groups and their values as options to filter variants by.

hasGraphicalPreview

hasGraphicalPreview = <boolean>

This property determines if the user can make a Graphical Preview request in the Genotype Browser for the study. This property takes a boolean value.

inheritanceTypeFilter

inheritanceTypeFilter = <comma-separated list of inheritance types>

This is a list of inheritance types that will be available as filters in the Genotype Browser for the study. You can see the available values here.

selectedInheritanceTypeFilterValues

selectedInheritanceTypeFilterValues = <comma-separated list of inheritance types>

This is a list of inheritance type filters that will be selected by default on a study’s page in the Genotype Browser. Note that these values must be present in the inheritanceTypeFilter property. You can see the available values here.

familyFilters

familyFilters = <>

selectedPhenoFiltersValues

selectedPhenoFiltersValues = <comma-separated list of pheno filter ids>

A comma-separated list of selected pheno filters. If this property is missing then all defined pheno filters in this section are selected.

phenoFilters.<pheno filter id>.name

phenoFilters.<pheno filter id>.name = <>

phenoFilters.<pheno filter id>.measureType

phenoFilters.<pheno filter id>.measureType = <>

phenoFilters.<pheno filter id>.filter

phenoFilters.<pheno filter id>.filter = <<filter_type>:<role>:<optional: measure>>

selectedPresentInRoleValues

selectedPresentInRoleValues = <comma-separated list of presentInRole ids>

A comma-separated list of selected presentInRole values. If this property is missing then all defined presentInRole values in this section are selected.

presentInRole.<present in role id>.id

presentInRole.<present in role id>.id = <present in role identifier>

Identifier of present in role. Default value is <present in role id> from the present in role property name.

presentInRole.<present in role id>.name

presentInRole.<present in role id>.name = <present in role name>

This property defines the display name of the Present in Role filter in the Genotype Browser for the study.

presentInRole.<present in role id>.roles

presentInRole.<present in role id>.roles = <comma-separated list of roles>

This property defines which roles are available to the Present in Role filter in the Genotype Browser for the study.

selectedGenotypeColumnValues

selectedGenotypeColumnValues = <comma-separated list of genotype column ids>

A comma-separated list of selected genotype columns. If this property is missing, then all defined genotype columns in this section are selected.

genotype.<genotype columns id>.id

genotype.<genotype columns id>.id = <genotype column identifier>

Identifier of the genotype column. Default value is <genotype column id> from the genotype column property name.

genotype.<genotype columns id>.name

genotype.<genotype columns id>.name = <genotype column name>

Display name of the genotype column used in the header of the table in the Table Preview query in Genotype Browser for the study.

genotype.<genotype columns id>.source

genotype.<genotype columns id>.source = <genotype column source>

This property defines the source of the values for this column. This is selected from the raw study data column names.

genotype.<genotype columns id>.slots

genotype.<genotype columns id>.slots = <<source>:<label>:<label_format>>

A genotype column can be split up into multiple sub-columns. These are called slots. Each slot is defined by:

  • <source> - analogous to the genotype.<genotype columns id>.source property above.

  • <label> - display name of this slot in the genotype column in the preview table in the Genotype Browser.

  • <label format> - format of the values in this slot. This property is optional and default value for it is %s.

selectedPhenoColumnValues

selectedPhenoColumnValues = <comma-separated list of phenotype column ids>

A comma-separated list of selected phenotype columns. If this property is missing then all defined phenotype columns in this section are selected.

pheno.<phenotype column id>.id

pheno.<phenotype column id>.id = <phenotype column identifier>

Identifier of the phenotype column. Default value is <phenotype column id> from the phenotype column property name.

pheno.<phenotype column id>.name

pheno.<phenotype column id>.name = <phenotype column name>

Display name of the phenotype column used in the header of the preview table in the Genotype Browser for the study.

pheno.<phenotype column id>.slots

pheno.<phenotype column id>.slots = <<role>:<source>:<label>:<label format>>

Slots of the phenotype column in the header of the preview table in the Genotype Browser for the study. Each slot is defined by:

  • <role> - apply the filter for people with this role.

  • <source> - the id of the phenotype measure whose values will be displayed.

  • <label> - display name of this slot.

  • <label format> - format of the values in this slot. This property is optional and the default value for it is %s.

inRoles

Each of the defined inRoles will be added to the variant as a new, generated column. This new column will contain information about defined roles in the inRoles.<in role column id>.roles. The resulting list will be all possible combinations of the role from roles list with the gender of the people with this role. The newly generated column can be optionally defined as a genotype column.

selectedInRolesValues

selectedInRolesValues = <comma-separated list of in role column ids>

A comma-separated list of selected inRoles columns. If this property is missing, then all defined inRoles columns in this section are selected.

inRoles.<in role column id>.id

inRoles.<in role column id>.id = <in role column identifier>

Identifier of the inRoles column. Default value is <in role column id> from the inRoles column property name.

inRoles.<in role column id>.destination

inRoles.<in role column id>.destination = <destination column name>

The name of the column in the variant which will contain the generated values. Default value for this property is inRoles.<in role column id>.id.

inRoles.<in role column id>.roles

inRoles.<in role column id>.roles = <comma-separated list of roles>

A comma-separated list of roles which will be used for the generation of the new column.

previewColumns

previewColumns = <comma-separated list of genotype or phenotype column ids>

Which columns to display in the preview table of the Genotype Browser of the study. Possible values in this list are genotype or phenotype column ids.

downloadColumns

downloadColumns = <comma-separated list of genotype or phenotype column ids>

Which columns to include in the download table file of the Genotype Browser of the study. Possible values in this list are genotype or phenotype column ids. Slots will be expanded into independent columns.