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, 14:49, 3 April 2012
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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. |
− | *[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
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− | *[[PolishBam]] – Add/Update header lines & add RG tag to each record
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| ==== BAM Util Tools ==== | | ==== BAM Util Tools ==== |
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| *[[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 |
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| '''Helper Tools to Print Readable Information''' | | '''Helper Tools to Print Readable Information''' |