Filter out reads whose mate maps to a different contig
This filter 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. If mates in a pair are mapping to different contigs, it is likely that at least one of them is in the wrong place. One exception is you are using a draft genome assembly in which the chromosomes are fragmented into many contigs; then you may legitimately have reads that are correctly mapped but are on different contigs than their mate. This read filter can be disabled from the command line using the -drf argument.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf BadMate
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -drf BadMate
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.