Filter out unmapped reads
This filter recognizes the SAM flag corresponding to being unmapped. 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 UnmappedRead
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.