# PeteHaitch/Correct-Bismark-SAM-BAM-FLAGs

> A Python script to "correct" the FLAGs in a SAM/BAM generated by Bismark to comply with the SAM specifications. Specifically, correct the strand information in the FLAG and add a custom tag XS:Z:<value> to encode which DNA-strand the read is informative for, where <value> = OT, CTOT, OB or CTOB.

- **Canonical URL**: https://githubrepo.cloud/repo/PeteHaitch/Correct-Bismark-SAM-BAM-FLAGs
- **GitHub Repository**: https://github.com/PeteHaitch/Correct-Bismark-SAM-BAM-FLAGs
- **Maintainer / Creator**: https://github.com/PeteHaitch
- **Discovered On**: Sep 27, 2026

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