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 theid
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+
andCNV*
effect types (part of theCNV
effect group) are present in theEffect Types
filter in theGenotype Browser
for the study.if the
CNV
,CNV+
andCNV*
effect types are present in theEffect Types
filter in thePhenotype Tool
for the study.if the
CNV
variant type is present in theVariant Types
filter in theGenotype 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 thegenotype.<genotype columns id>.source
property above.
<label>
- display name of this slot in the genotype column in the preview table in theGenotype 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.