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Filter out reads that are secondary alignments

Category Read Filters


This filter recognizes the SAM flag that identifies secondary alignments (ie not the best alignment). It is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis.

Usage example

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

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