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Only use reads from the specified read group

Category Read Filters


This filter is useful for isolating data from one particular read group (usually a single lane).

Usage example

Use only reads from the read group with ID "read_group_1

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf SingleReadGroup \
         -goodRG read_group_1

Command-line Arguments

SingleReadGroupFilter specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Required Parameters
NA The name of the read group to keep, filtering out all others

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--read_group_to_keep / -goodRG

The name of the read group to keep, filtering out all others

R String  NA

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