SAM/BAM export format specification


SAM Specification The workbench aims to import and export SAM and BAM files according to the v1.4-r962 version of the SAM specification (see This appendix describes how the workbench exports SAM and BAM files along with known limitations.

SAM and BAM Export - General notes

The SAM exporter writes unsorted SAM and BAM files.

If the reference name contains spaces, the spaces are removed. Each occurrence of '=' (equals sign) and '@' (at sign) in a reference name is replaced by an '_' (underscore).

The SAM importer and exporter support the ID, SM, PI and PL read group tags. All other read group tags are ignored.

The BAM exporter can also output additional annotations added by tools provided by plugins, and where that is the case, further details are provided in the plugin manual.

SAM Alignment Section A few remarks on the exported alignment section:

Optional fields in the alignment section The following is true for the export of optional fields: