Filter out reads produced by 454 technology
Reads produced by 454 technology should not be processed by the GATK's indel realignment tools. This filter is applied by those tools to enforce that rule.
java -jar GenomeAnalysisTk.jar \ -T ToolName \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf Platform454
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.