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*[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
*[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
*[[PolishBam]] – Add/Update header lines & add RG tag to each record
*[[PolishBam]] – Add/Update header lines & add RG tag to each record
==== BAM Util Tools ====
The following tools are part of the [[BamUtil|BamUtil program]].
The following tools are part of the [[BamUtil|BamUtil program]].
'''QC/Stats'''
'''QC/Stats'''
*[[BamUtil: validate|validate]] – Check file format & print statistics
*[[BamUtil: validate|validate]] – Check file format & print statistics
*[[BamUtil: squeeze|squeeze]] - Reduce files 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: squeeze|squeeze]] - Reduce files 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: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap
*[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap
*[[BamUtil: trimBam| trimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
'''Helper Tools to Print Readable Information'''
'''Helper Tools to Print Readable Information'''
*[[BamUtil: dumpHeader|dumpHeader]] - Print the File Header to the screen.
*[[BamUtil: dumpHeader|dumpHeader]] - Print the File Header to the screen.
