Roslin Bioinformatics - Genotype Checker

Workflow

  1. start application (see Running GenotypeChecker)
  2. load pedigree file (see Loading Data)
  3. Displays Pedigree and Reports Pedigree Metrics
    Fails if invalid data
  4. load genotype file (see Loading Data)
  5. Displays Table of Markers
    Fails if invalid data
  6. check consistency of all markers (or proceed straight to 5.)
  7. Reports Inconsistent Markers
  8. select markers for analysis, optionally segmenting into manageable segments
  9. inheritance check the selected markers, optionally segmenting into manageable segments (see Inheritance Checking)
  10. Displays sortable table of inconsistencies
  11. explore data to isolate source of inconsistency
  12. The immediate family context of an individual can be examined (see Family Views)
  13. mask suspect data (genotypes, individuals or markers) and recheck the inheritance (see Inheritance Checking)
  14. export metrics reports and final clean (masked) dataset (see Saving Data)

Overview

The inheritance checked data is colour coded to allow easy recognition of problematic Markers and Individuals (red for inconsistent Genotypes, yellow and green for partially and totally resolved inferred Genotypes).

The data displayed in the results table can be sorted in a variety of ways (by Individual name, Generation, number of total errors, number of errors for a particular Genotype etc) by clicking on column headers.

To improve readability Individuals and Markers can be hidden in the display, but to allow the cause of inheritance inconsistencies to be investigated specific Individuals, Genotypes or whole Markers can be 'masked'. Masked data is ignored when the Pedigree is rechecked. In this manner it is possible to identify the exact problematic Genotype that is causing inheritance errors throughout the Pedigree.

For convenience it is possible to save an edited copy of the input genotype data file, from which all masked datapoints have been removed. This provides a simple way of cleaning the genotype information prior to downstream processing.

As well as providing the interactive tabular display of the whole Pedigree, it is possible to focus on particular Individuals of interest and generate tabular views of its inheritance in the context of close relatives ('Family Views': 'Full Sibs', 'Sire Sibs' and 'DamSibs'). These sub displays are linked to the full display, so that interaction performed on any view apply across all of the views.

The 'Messages' Tab

Information and error messages are displayed in the 'Messages' tab. These are updated with every action performed (e.g. loading data, parsing data, checking data). The current message can be printed using the 'Print Report' button.The current message (together with other reports) can also be saved as an HTML file using the 'Save Report' button or 'Report' menu item, to a location of choice (see Saving Data).