Changes

This program is part of the [[Software#StatGen_C.2B.2B_Software| StatGen Library & Tools]] [[StatGen Download|download.]]

This program is part of the [[Software#StatGen_C.2B.2B_Software| StatGen Library & Tools]] [[StatGen Download|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 program 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.

SuperDeDuper is a standalone application that may be used in the following way.  Please note that the records in the input BAM file are assumed to be sorted by coordinate.  The various options are explained below.

SuperDeDuper is a standalone application that may be used in the following way.  Please note that the records in the input BAM file are assumed to be sorted by coordinate.  The various options are explained below.