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 3.7-0-gcfedb67 built at 2017/02/09 12:35:06.