3,045
edits
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==== Update the File ====
==== Update the File ====
[[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
*[[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
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[C++ Executable: bam#filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
*[[C++ Executable: bam#filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
==== Split the File ====
==== Split the File ====
