Analyses

Owned by Yaw Nti-Addae
Last updated: Nov 18, 2020 by Joel ByrnesVersion comment
2 min read

Definitions

Analyses describe the different algorithms that were applied to the genotyping or sequence data to produce the final dataset being loaded. Each analysis is grouped into an analysis type. The analysis types are: calling (variant calling), cleaning, and imputation. Additional analysis types can be added in Controlled Vocabularies: Define | Controlled Vocabulary | analysis_type.

Field Descriptions

  • Analysis Type: Mandatory field describing the type of analysis. Select from a pull-down menu. You can add additional Analysis Types in Define | Controlled Vocabulary | analysis_type. 
  • Analysis Name: Mandatory field for the name of the analysis. The analysis name must be unique within each analysis type.
  • Analysis Description: Optional field for the analysis description.
  • Program: Optional field describing the program used to perform the analysis. For example, Tassel.
  • Program version: Optional field for the version of the program. For example, 5.0.
  • Source Name:��Optional field for the source name of the program.
  • Source Version: Optional field for the version of the source name.
  • Source URL: Optional field for the URL of the source name.
  • Parameters: Optional fields defined by the curator that describe the parameters and values used in the analysis.

Add a New Analysis

  1. From the menu bar, select Define | Analyses. A list of existing analyses display on the left side of the form. Export exports a text file of the analyses listed.
  2. Select an analysis type from the Analysis Type drop-down menu on the left side of the form. Currently analysis types are: allele_sorting (for haplotype specific calls), calling (variant calling), cleaning (data cleaning methods), or imputation. Analysis type is defined in Define | Controlled Vocabulary | analysis_type. 
  3. For your new analysis, enter the analysis name in the Analysis Name field. 
  4. Optionally add the analysis description, program, program version, algorithm, source name, version, and URL in the applicable fields.
  5. Optionally add parameters. Click New Parameter. Next to the checkbox, enter the applicable parameters and values.
  6. Add a reference if a specific reference genome was used in the analysis. Your reference should be previously defined by using Define | References.
  7. Click Add New. If the request is successful, a confirmation message displays and the name of the new analysis displays on the left side of the form.


Update an Existing Analysis

  1. From the menu bar, select  Define | Analyses. A list of existing analyses display on the left side of the form.
  2. Select an analysis type from the Analysis Types drop-down menu on the left side of the form. 
  3. Select the analysis you want to update. 
  4. Edit any applicable fields. 
  5. Click Update. If successful, a confirmation message displays.