Filter out reads that are secondary alignments
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.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf NotPrimaryAlignment
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.