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Quality control for the reference fasta

Category Reference Utilities

Traversal LocusWalker

PartitionBy LOCUS



One reference file only. And optionally -L intervals


If the reference is fully valid, the run will complete successfully. If not, an error message will be produced at the site where the program encountered a problem.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T QCRef \
   -R reference.fasta

Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by QCRef.

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

QCRef 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
Optional Outputs
stdout An output file created by the walker. Will overwrite contents if file exists

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.

--out / -o

An output file created by the walker. Will overwrite contents if file exists

PrintStream  stdout

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