Showing docs for version 3.6-0 | The latest version is 4.1.4.0


DuplicateReadFilter

Filter out duplicate reads

Category Read Filters


Overview

This filter recognizes the SAM flag set by MarkDuplicates. It can be disabled from the command line if needed using the -drf argument.

Usage examples

Enable the duplicate read filter

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf DuplicateRead
 

Disable the duplicate read filter

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -drf DuplicateRead
 

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.