Filter out reads with bad pairing (and related) properties
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. The following cases will be filtered out:
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf MateSameStrand
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.