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.

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: