Filter out reads without read group information
Many GATK tools are dependent on having read group information in order to operate correctly. This filter excludes any reads that have not been appropriately identified.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf MissingReadGroup
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.