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*[[SuperDeDuper]] - Determine duplicate alignments, either marking or removing the lower quality duplicates. In addition, it may modify paired-end reads where the ends overlap by soft clipping the end with the lower quality bases in the region of overlap.
*[[SuperDeDuper]] - Determine duplicate alignments, either marking or removing the lower quality duplicates. In addition, it may modify paired-end reads where the ends overlap by soft clipping the end with the lower quality bases in the region of overlap.
==== BAM Util Tools ====
==== BAM Util Tools ====
*[[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 ‘!’
*[[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
'''Helper Tools to Print Readable Information'''
'''Helper Tools to Print Readable Information'''
