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Only use reads belonging to a specific sample

Category Read Filters


This filter is useful for isolating data from one particular sample in a multisample file.

Usage example

Use only reads from the sample named NA12878

     java -jar GenomeAnalysisTk.jar \
         -T ToolName \
         -R reference.fasta \
         -I input.bam \
         -o output.file \
         -rf Sample \
         -goodSM NA12878

Command-line Arguments

SampleFilter 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 sample(s) 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.

--sample_to_keep / -goodSM

The name of the sample(s) to keep, filtering out all others

R Set  NA

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