23. April 2012 · Comments Off on Manual genotype calling in Evoker · Categories: Software · Tags:

Version 2.2 of the Evoker software has just been released through sourceforge and is available to download here.

This is a major new release of Evoker as it includes an important new feature, users now have the ability to manually recall the genotypes of any marker in a dataset. A number of other general improvements and bug fixes are also included in this latest release.

Genotype calling is an automated process which can produce errors, below is an example of how such errors appear when loaded in Evoker.
poorly called marker
Using the latest version of Evoker it is now possible to correct such errors with manual calling.

Here is a step by step guide of how to go about manually recalling such a marker:

  • Step 1: First enter Lasso Select mode
    enter lasso mode
    To do this simply right click on the plot area and select select lasso mode from the popup menu.
  • Step 2: Select individuals to change
    lasso select individuals
    Press the mouse button and draw a lasso around the individuals you wish to recall.
  • Step 3: Change the genotype
    select new genotype
    Select the genotype you would like to assign to the selected individuals from the popup menu.
  • Step 4: The genotypes are successfully altered
    genotypes are now altered
    Now repeat these steps until you are happy with the genotype calls for all the individuals.
  • Step 5: Save the changes
    save changes
    Changes are saved in memory so you do not need to save after each marker. When you are ready to save the changes made to a single collection select ‘Save BED…’ from the File menu and then select the collection you wish to save. If you are working with multiple collections it is also possible to save changes in all collections in one go using the ‘Save All BEDs’ option also in the File menu.
  • Step 6: Saved files
    saved files
    Saved files will be created in the location you select for every chromosome containing an altered marker. If you use the ‘Save All BEDs’ option new files will be generated in the original data directory with MOD added to the filename.
  • The manual calling feature is currently only available for data that has been loaded locally.

    The bulk of the work for getting manual calling working in Evoker was done by Natalie Wirth a visiting student.

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