Ngs RemoveDuplicates.pdf

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Remove Duplicates for NGS Data

This module removes duplicates in a DNA-Seq data file. In NO circumstances is this module recommended for RNA-Seq data.

Duplicates are defined by alignments with the same start position and end position, or fragments with same range (start and end positions of read1 and read2 in a pair).

Open this module by going to NGS | Manipulation | Remove Duplicates

Ngs RemoveDuplicatesForNgsData 1.png


  • Mark duplicates only - Mark the duplicates using bitwise SAM flags in the resulting BAM file instead of removing them.
  • Output folder - Specifies the output folder for the new BAM file to be generated.


The output of this module is a BAM file generated in the specified folder with duplicates removed or marked from the original BAM file.