By default, IGV displays tracks in the order in which they are loaded (i.e., the order of the data in the files). Alternatively, it is possible to sort the tracks by attribute, region of interest, or track list. You can also group or filter tracks.

Sorting by Attribute

If tracks are grouped, IGV sorts the tracks in each group. To sort groups by attribute, first sort the ungrouped tracks by the desired attributes, then group the tracks.

To sort tracks based on an attribute value:

• Click the attribute name in the attributes panel. IGV sorts the tracks based on the attribute's value.

Alternatively, use the Sort Tracks command for additional options:

1. Click Tracks>Sort Tracks. IGV displays the Sort window:
   
2. Select the attributes to sort by and whether to sort based on ascending or descending values.
3. Click Ok.

Sorting by Region of Interest

If tracks are grouped, IGV sorts the tracks in each group. It then sorts the groups using a composite score for the group, which IGV defines as the maximum score from the tracks in that group.

To sort tracks in the data panel based on a region of interest:

1. Define a region of interest on the genome, as shown below.
2. Click the red bar above the defined region and select an option from the pop-up menu:
   • Sort by amplification: Affects tracks of copy number data. Sorts tracks based on copy number values in this region, from highest to lowest.
   • Sort by deletion: Affects tracks of copy number data. Sorts tracks based on copy number values in this region, from lowest to highest.
   • Sort by breakpoint amplitudes: Affects tracks of copy number data.  Sorts tracks by the sum of the absolute value of copy number changes within the region.
   • Sort by expression: Affects tracks of gene expression data. Sorts tracks based on gene expression in this region, from highest to lowest.
   • Sort by value: Sorts tracks based on the values of the track data in this region, from highest to lowest.
   • Delete: Removes this region-of-interest annotation.

Sorting and Filtering by Track List

To display selected tracks in a specific order:

1. Create a sample information file that contains two columns. The first column must be labeled 'Array' and lists the tracks that you want to display. The second column can be labeled 'Order' (or any other label) and lists the sort order for the tracks.
   For example, the following sample information file provides a track list for use with segmented_data_080520.seg:
   

   Array	Order
   primary_GBM_10	a
   primary_GBM_20	b
   primary_GBM_30	c
   primary_GBM_40	d
   primary_GBM_50	e
   primary_GBM_60	f
   primary_GBM_70	g

2. Load the data file and the sample information file that you created in step 1.
3. Apply a filter to display only those tracks that contain a value for the Order attribute. To do so, select Tracks>Filter Tracks and apply the following filter:
   Order is not equal to <leave the text field blank>
4. Sort the tracks based on the Order attribute. To do so, select Tracks>Sort Tracks and select the Order attribute.

Grouping Tracks by Attribute

To group tracks by attribute:

• Select Tracks>Group Tracks and choose an attribute from the drop-down list. IGV organizes the tracks into groups that share the same value for that attribute.

Filtering Track Data

You can filter track data to display only tracks that meet certain criteria.

To filter tracks:

1. Select Tracks>Filter Tracks. IGV displays the Filter Tracks window:
    
2. Enter a filter criterion by selecting an attribute from the first drop-box and an operator from the second drop-box and entering an attribute value in the text box.
3. Optionally, add additional criteria:
   • Click the plus (+) button to enter another filter criterion.
   • Click the minus (-) button to remove a filter criterion.
4. Determine how the criteria should be combined by choosing one of the following, at the top of the window:
   • Match all of the following to combine the criteria using a logical AND
   • Match any of the following to combine the criteria using a logical OR
5. Click OK to apply the filter.

To clear the filter:

1. Select Tracks>Filter Tracks.
2. At the top of the Filter Tracks window, click Show all tracks, then click OK.