Ion Torrent™ BAM format

Ion Torrent™ BAM files follow the conventions of the SAM/BAM Format Specification Working Group. SAM stands for Sequence Alignment/Map.

The following highlights specific Ion Torrent™ conventions and the meaning of custom tags.

Run ID: Every TS analysis assigns a run ID, a 5-character string consisting of upper case letters and numbers. A reanalysis of a specific run assigns a different run ID. Example: 0JU8V.
Read Group ID: For non-barcoded runs the read group ID is equal to the run ID. For barcoded runs it is a combination of the run ID and the barcode name, which is separated by a dot. Example: 0JU8V.IonXpress_001.
Key Sequence (KS): For non-barcoded runs, the Key Sequence tag is the Ion Torrent™ library key (TCAG). For barcoded runs the KS tag entry includes the barcode sequence and the barcode adapter sequence if barcode trimming is enabled.
Reverse Key Sequence (sk): For dual-barcoded runs, the Reverse Key Sequence tag includes the end barcode adapter sequence and the end barcode sequence.
SAM record (read) names: Read names are a combination of the run ID and the chip coordinates of the well that produced the read. The coordinate values are 5-digit numbers and are given in the order row and the column, which is separated by a colon. Example: 0JU8V:01308:00107.
BAM header comment lines (CO): Comment lines in the BAM header are used to store base calibration information, or information about the 3' adapter sequences.