To compare samples in a run

Geneticist Assistant Online Help : Common Procedures : Comparing Samples in a Run : To compare samples in a run

1. Do one of the following:

• From the Runs tab: Right-click the appropriate run on the runs tab, and on the context menu that opens, click Compare Samples.

The Sample Comparison dialog box opens. All the samples for the selected run are displayed in the dialog box.

• From the Run tab:

i Open the Run tab for the appropriate run.

ii. CTRL-click to select the samples in the Samples pane that you are comparing,

iii. Right-click any selected sample and on the context menu that opens, click Compare Samples.

The Sample Comparison dialog box opens. All the selected samples for the run are displayed in the dialog box.

2. Set the comparison parameters.

Option	Description
Show columns	The data columns that are displayed for each sample on the Sample Comparison tab. Allele Frequency (AF) is always displayed and you cannot change this option. By default, Coverage (Cov) is selected.
Filter variants by panel	Limits the variants that are displayed don the Sample Comparison tab to only those variants that are contained within the selected panel.
Filter variants by pathogenicity	Limits the variants that are displayed on the Sample Comparison tab to only those variants with the selected pathogenicity.
Shared by	Limits the variants are displayed on the Sample Comparison tabl to only those variants that meet the required number of samples as specified by the operator that is selected on the dropdown list (>, <, or =) and the number of samples. If a variant is found a number of samples that does meet this criteria, then the variant is not displayed in the results.
AF difference	Limits the variants are displayed on the Sample Comparison tabl to only those variants that meet the required number of samples as specified by the operator that is selected on the dropdown list (>, <, or =) and the AF difference value. If a variant is found a number of samples that does meet this criteria, then the variant is not displayed in the results.
• Exclude missing variants	Selected by default. Regardless of the allele frequency difference, always display variants that are not found in one or more samples.
AF between	Limits the variants that are displayed on the Sample Comparison tab to only those variants with an allele frequency (AF) that falls within the indicated range in at least one of the compared samples.

3. Click OK.

The Sample Comparison dialog box closes. The Sample Comparison results are displayed on the Sample Comparison tab. The far right side of the tab shows the sample-specific information for each variant, with each sample identified as 1, 2, and so on. If you hover your cursor over the column heading, then the full sample name is displayed. The left side of the tab shows the variant information.