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Count the total number of covered loci

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


This tool counts the number of loci (positions in the reference) that are covered by sequence data.


One or more BAM files.


Number of loci traversed. If an output file name is provided, then the result will be written to that file. Otherwise it will be sent to standard console output.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T CountLoci \
   -R reference.fasta \
   -I input.bam \
   -o output.txt \
   [-L input.intervals]

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using these options.

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.

CountLoci 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.