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Filter out reads matching a read group tag value

Category Read Filters


This filter is useful for running on only a subset of the data as identified by a read group property, using expression matching against the read group tags.

Usage example

Set the read group filter to blacklist read groups that have the PU tag "1000G-mpimg-080821-1_1"

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf ReadGroupBlackList \
         -rgbl PU:1000G-mpimg-080821-1_1

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.