Only use reads with this read name

Category Read Filters


This filter is useful for isolating a particular read, pair of reads or or set of alignments for a given read when troubleshooting issues where the error message provided a culprit name.

Usage example

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf ReadName \
         -rn read_name

Command-line Arguments

ReadNameFilter 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 Read name to whitelist

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.

--readName / -rn

Read name to whitelist

R String  NA

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GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.