Flags

The workbench's use of the alignment flags is shown in the following table and subsequent examples.

Bit SAM description Usage in Workbench
0x1 template having multiple segments in sequencing set if the segment is part of a pair
0x2 each segment properly aligned according to the aligner set if the pair is not broken
0x4 segment unmapped never set since the exporter does not export unmapped reads
0x8 next segment in the template unmapped never set by the exporter. If a segment has an unmapped mate, the flag 0x1 is not set for the segment, i.e.is not output as part of a pair
0x10 SEQ being reverse complemented set if and only if the segment was reverse complemented during mapping
0x20 SEQ of the next segment in the template being reversed set if and only if the mate was reverse complemented during mapping
0x40 the first segment in the template this mate is the first segment of the pair
0x80 the last segment in the template this mate is the second segment of the pair
0x100 secondary alignment never set by the exporter and ignored by the importer
0x200 not passing quality controls never set by the exporter and ignored by the importer
0x400 PCR or optical duplicate never set by the exporter and ignored by the importer



Subsections