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Read Stitching
A stitched read is a single read that has been bioinformatically stitched from a pair of reads. The ReadStitcher takes paired reads from a BAM, stitches them, and writes out a new BAM. Reads that cannot be stitched are left unchanged.
The stitched read contains the following:
| • | one consensus sequence of base calls. |
| • | one consensus sequence of base call qualities. |
| • | one consensus cigar string. |
| • | one direction tag. |
The direction tag gives the original directions of the contributing reads.
To save on future processing time, the ReadStitcher filters out reads that are not used downstream, such as PCR duplicates or poorly mapped reads. The pipeline performs sorting and indexing of output stitched BAM.
For Research Use Only. Not for use in diagnostic procedures.