Ion Torrent reads provided either as un-mapped or mapped reads in .BAM or .SAM format can be imported as a Read List using the Ion Torrent High-throughput sequencing importer:

Import | Other NGS Reads | Ion Torrent 

This importer is described on the following manual page: 
Ion Torrent


Other Mapped reads, e.g. Illumina, GeneReader, provided in .BAM or .SAM format can be imported as a read list using the Standard importer:

Import | Standard import

Please leave the import type set to Automatic.

After completing the import wizard, a popup window will appear asking if you would like to skip importing this BAM or SAM file. Please click No in this popup window.



The imported reads from the .BAM or .SAM file will either be a single Read List, or multiple Read Lists - one for each Read Group in the .BAM or .SAM file. 

After import go to the Element Information view of your Read Lists to check that the platform and distance range set settings are appropriate for your data.

Relevant manual pages regarding this can be found here:

• Standard import
• Import high-throughput sequencing data
• Sequence Lists
• History and Elements Info views
• Element information