BAM feature filters

When you right-click on a BAM track in the Genome Browser, a context menu appears that allows you to view the currently displayed results in a table. Selecting View in table… will display a menu of different feature filters that can be used to view the results.

The basic query that is used to open the data is as follows:

gor -p <your_position_info> <path_to_BAM_file> | where qname in ('<qname_of_individual_read>')

In a default installation, there are three different filters displayed here, but these can be configured to include any queries you wish.

The three filters included in the default installation are shown in the table below.

BAM feature filters

Filter name	Description
Expand flags	Shows additional information on the selected reads
Strand error	Find reads where both items in a pair are reported on the same strand
Forward/Reverse	Pileup for forward and reverse strand