Filter out duplicate reads
This filter recognizes the SAM flag set by MarkDuplicates. It can be disabled from the command line if needed using the -drf argument.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf DuplicateRead
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -drf DuplicateRead