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Settings
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Most of Gravity's settings are stored in the form of Cytoscape properties files and are totally transparent to the user (*i.e.* saving the default filters). However for some more specific functionalities, you might need to edit a Cytoscape property file as explain here.

In Cytoscape, go to *Edit -> Preferences -> Properties...*

In this new window select the *Gravity.gravity* properties.

.. figure:: images/settings/properties_editor.png
  :figclass: align-center

  *Cytoscape property editor.*

It displays a list of properties that can be edited based on your needs. This section will describe them and explain the accepted values.

BAM server
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The *Gravity.settings.BAMserver* property allows to define a web URL to open in the system browser when the user double click a variant in GRAVITY. We defined this to allow the BAM file visualisation in a local instance of IGV that can display informations for all our cohorts.

The default value is *http://gravity.pasteur.fr/pileup/?chr=%CHR%&start=%START%&end=%END%&individuals=%INDIVIDUALS%* and allow you to visualise the BAM from the sample

In this URL code we offer several wildcards for the following:

* *%LOCUS%* will be replaced by *chromosome:position*
* *%CHR%* for the chromosome
* *%START%* for the position of the variant minus hundred nucleotides
* *%END%* for the position of the variant plus hundred nucleotides
* *%POSITION%* as an alias for *%CHR%:%START%-%END%*
* *%INDIVIDUALS%* for a semicolon separated list of individuals (selected individuals and his/her parents)
* *%FAMILY%* will be replaced by the FID from the pedigree from the currently displayed family.

Population frequency
--------------------

These option will allow you to define which field from your VCF to use for the population and cohort frequency. You can enter multiple names separated by semicolons, in such a case, the first one found will be used.

The *Gravity.settings.PopulationFrequency* property is used for the population frequency, by default we are using gnomAD frequency with a few predefined names.

The *Gravity.settings.CohortFrequency* property is used for the cohort frequency, by default it is using the AF field from the VCF, but other option could be added, particularly if you are computing a founder or control frequency on your own.

Deleteriousness
---------------

We offer an option for a quick display of a deleteriousness value. By default we are using the CADD score, but any value can be used. Two fields need to be filled, the first one *Gravity.settings.DeleteriousnessName* will contain the label displayed in GRAVITY's interface, while the second *Gravity.settings.DeleteriousnessField* will contain the name of the VCF field to use. Similarly to the frequencies, a semicolon separated list can be used for the field name, which allow for several attributes options in case of non standardised pipeline.