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From Genome Analysis Wiki
→Programs
** [[BamUtil: squeeze|'''squeeze''' - Reduce file size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]
** [[BamUtil: trimBam|'''trimBam''' - Trim end of reads, changing read ends to ‘N’ & quality to ‘!’]]
**[[BamUtil: polishBam|'''polishBam''' – Add/Update header lines & add RG tag to each record]]
**[[BamUtil: rgMergeBam|'''rgMergeBam''' – Merge sorted BAM files adding Read Groups]]
* Informational Tools
