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= SuperDeDuper =
= SuperDeDuper =
This class is part of [[C++ Library: libStatGen]].
This program is part of the [[StatGen Download|StatGen Library & Tools download.]]
This class will read a BAM file, determine duplicate alignments, and either mark or remove 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. A few additional features are coming soon.
This class will read a BAM file, determine duplicate alignments, and either mark or remove 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. A few additional features are coming soon.
