Indel Realignment and Read Stitching

The Gemini software component performs local indel realignment, paired‑read stitching, and read filtering. A stitched read is a single read that has been combined from a pair of reads. Reads near detected indels are realigned to remove alignment artifacts. The input is a single BAM file and the reference genome FASTA used to align it; the output is a corresponding single BAM file with stitched, pair‑realigned reads. Read pairs with poor map quality or supplementary and secondary alignments from the input BAM are ignored.

The following BAM tags are added to the stitched reads:

•

XD—Directional support string indicating forward, reverse, and stitched positions.

•

XR—Read pair orientation, which can be either forward-reverse (FR) or reverse-forward (RF).