SAM/BAM/CRAM export format specification


The CLC Genomics Workbench aims to import and export SAM and BAM files according to the v1.4-r962 version of the SAM specification (see, and CRAM files according to the v3.1 version of the CRAM specification (see This appendix describes how the CLC Genomics Workbench exports SAM, BAM and CRAM files, along with known limitations.

General notes about the exporters

The exporters write unsorted SAM/BAM/CRAM files.

Reference names are updated to match the SAM specification:

The following read group tags are supported: ID, SM, PI and PL. All other read group tags are ignored.

The exporters can also output additional annotations added by tools provided by plugins. Where that is the case, further details are provided in the plugin manual.

Alignment Section

Here are a few remarks on the alignment sections of the exported files:

Optional fields in the alignment section

The following is true for the export of optional fields: