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 http://samtools.sourceforge.net/SAM1.pdf). 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:
- Unmapped reads are not exported.
- If pairs are not on the same contig, the mates will be exported as single reads.
- Multi segment mappings will be imported as a paired data set.
- If a read name contains spaces, the spaces are replaced by an underscore '_'.
- The exported CIGAR string uses 'M' to indicate match or mismatch and does not use '=' (equals sign) or 'X'.
- CLC software does not support or record mapping quality for read mappings. To fulfill the requirement in the BAM format specifications that a read mapping quality is recorded for all mapped reads, the values 0 and 60 are used when mappings are exported from the Workbench. The value 60 is given to reads that mapped uniquely. The value 0 is given to reads that could map equally well to other locations besides the one being reported in the BAM file.
This scoring system is based on a recommendation provided in the the SAM FAQ:
Optional fields in the alignment section The following is true for the export of optional fields:
- The NH tag is exported.
- The NM tag is not exported.
- The workbench exports color space information in the CS tag.
- The colors of a right mate are incorrect since the colors of a paired read are stored as a single color string.
- For hard clipped sequence reads, the color space is incorrect, since the color space string is not hard clipped.
- SAM files contain sequence quality score and color quality
scores. The workbench only have color quality scores and these are
stored and exported as sequence quality scores.