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Only use reads from the specified library

Category Read Filters


This filter is useful for running on only a subset of the data as identified by a read group property. In the case of the library filter, the goal is usually to run quality control checks on a particular library.

Usage example

Enable the library read filter

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf LibraryRead \
         -library library_name

Command-line Arguments

LibraryReadFilter 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 library 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.

--library / -library

The name of the library 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.