Roslin Bioinformatics - Genotype Checker

Genotype Checking (with or without 'Masking')

The Genotype Checking algorithm is applied by pressing the 'Check Genotype' button in any of the 'Pedigree + Genotypes', 'Markers' or 'Checked Pedigree' Tabs. The algorithm will ignore any 'Masked' Genotypes - but will not ignore hidden rows and columns. Upon completion a report is generated and displayed in the 'Messages' Tab, and a new Tab 'Checked Pedigree' opened. The data and controls displayed in this view are similar to that of the 'Pedigree + Genotypes' Tab, but now the data has had Genotype checking and inference applied.

New (sortable) table columns record the total number of inconsistent ('Bad') Genotypes for each Individual, and the number of Genotypes that have been refined by inference. The actual Genotype data Cells are coloured: Red for reported inconsistencies, Yellow for Genotypes partially resolved by Inference (based on parent and descendant Genotypes) and Green for fully resolved Genotypes. Mouse 'Hover' over coloured cells displays a report on that Genotype cell, and any cell can be selected to display a detail message in the 'Selected Cell' message pane. Data Rows are again sortable by clicking on the Column Headers - but now the Marker columns sort by 'error' (i.e. red cells are put at the top or bottom). Additionally the order of the columns has been changed to push those with the highest number of errors to the left of the display. Columns can be dragged, resized and hidden as in the previous Tab, and masking can be applied by selecting (left-clicking) a column header, an 'individual' cell, or one or more 'genotype' cells (control+left-click for multi-selection), then selecting the sub-menu by right-clicking and selecting 'Mask'. (Masking applied to data in any view Table is applied to the other Tables).

The Overview Tab

In order to visualize the whole genotyped dataset (i.e. the active chunk if data is segmented) a further Tab is displayed upon genotype checking: 'Checked Overview'. This view presents a minimized view of the table data in the 'Checked Pedigree' Tab. Columns are again sortable to move 'Bad' Genotypes up or down, and Row and Column sizes can be altered for readability. No Interaction is provided in this table, but Genotypes are displayed upon Mouse Hover over a Cell of interest. Currently sorting Rows in this table is not linked to the ordering of Rows in the Checked Pedigree' table.

Rechecking Data

By activating the 'Recheck Genotype' button in the 'Checked Pedigree' Tab, rechecking of the Genotypes is applied. Typically this would be done following the masking of any individual Genotypes, complete Genotype data for an Individual, or all Genotypes for a Marker etc. (see above). The masked genotypes are ignored by the rechecking algorithm, and any genotypes given after rechecking will be derived solely form inference - not from the original input data. This is a useful tool for investigating which particular genotype is causing problems in the Pedigree. The rechecked data is redisplayed in the 'Checked Pedigree' and 'Checked Overview' Tabs, and masking is maintained.