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configuration.md

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GSvar configuration

INI files

The main configuration of GSvar is done via INI files located in the same folder as the GSvar executable.

Since these files can contain sensitive information like passwords, it is possible to encrypt information in the settings file.

settings.ini

This file contains basic settings that are used for all ngs-bits applications. If it is missing, copy the example file:

cp settings.ini.example settings.ini

The settings are:

  • reference_genome: the path to the reference genome FASTA file
  • ngsd_...: Database credentials for the NGSD (if available)
  • genlab_...: Database credentials for the GenLab (if available)
  • projects_folder_...: Prject data folders for different project types (diagnostic, research, test, external)
  • data_folder: megSAP data folder used to find target region BED files of processing systems

GSvar.ini

This file contains settings specific for GSvar. If it is missing, copy the example file:

cp GSvar.ini.example GSvar.ini

The most important settings are:

  • build: Genome build to use. Default is hg38.
  • threads: number of threads used
  • clinvar_api_key.: API key for Clinvar upload of variants
  • analysis_steps_...: Analysis steps of queuing of analysis on cluster for different analysis types
  • proxy_...: Proxy settings (if needed)
  • gsvar_...: Output folders for different documents GSvar creates, e.g. reports.
  • igv_menu: A comma separated list of IGV custom tracks. Each track consists of these tab-separated parts:
    • track name
    • checked by default (0 or 1)
    • path to track file
  • email_run_...: semicolon-separated list of additional email addresses that are used when the email button on the run tab is pressed.
  • custom_menu_small_variants: tab-separated list of custom context menu entries. Each entry constists of name|URL. The name is shown in the context menu. The URL is opened and the following strings are replaced by values from the variant: [chr], [start], [end], [ref], [obs].
  • gsvar_file_outdated_before: GSvar files created before the given date (yyyy-mm-dd) cause a user warning stating that they are outdated.

Filters

Default filters can be defined using these files, located in the same folder as the GSvar executable.

GSvar_filters.ini

Default filters for small variants.

Lines that start with # define a filter name. All lines after that don't start with # contain filter steps.

Lines that contain #--- insert a separator. They are used to group filters.

Filter names and parameters are described here.

GSvar_filters_cnv.ini

Default filters for CNVs.

Lines that start with # define a filter name. All lines after that don't start with # contain filter steps.

Lines that contain #--- insert a separator. They are used to group filters.

Filter names and parameters are described here.

GSvar_filters_sv.ini

Default filters for SVs.

Lines that start with # define a filter name. All lines after that don't start with # contain filter steps.

Lines that contain #--- insert a separator. They are used to group filters.

Filter names and parameters are described here.

Other files

GSvar_special_regions.tsv

This file contains special regions for sub-panel design.

Normally, sub-panels are designed a coding regions plus 5 to 20 flanking bases. However, some genes contain known pathogenic variants in intronic or intergenic regions. These non-coding but important regions can be specified in this file.

Each line starts the a gene name followed by one or more regions in the format chr:start-end.

Note: The separator used is tab, also between regions!

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