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Count the number of ROD objects encountered along the reference

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


CountRodsByRef is a RefWalker, and so traverses the data by position along the reference. It counts ROD elements (such as, but not limited to, variants) found at each position or within specific intervals if you use the -L argument (see CommandLineGATK).

Note that this tool is different from the basic CountRods, which is a RODWalker, and so traverses the data by ROD. For example if the ROD passed to it is a VCF file, CountRods will simply count the variants in the file.

Both these tools are different from CountVariants in that they are more generic (they can also count RODs that are not variants) and CountVariants is more detailed, in that it computes additional statistics (type of variants being indels vs. SNPs etc).


One or more ROD files.


Number of RODs seen.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T CountRODsByRef \
   -R reference.fasta \
   -o output.txt \
   --rod input.vcf

Additional Information

Read filters

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

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.

CountRODsByRef 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 Inputs
[] Input VCF file(s)
Optional Flags
false If true, this tool will print out the skipped locations
false If true, this tool will print out detailed information about the rods it finds and locations

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.

--rod / -rod

Input VCF file(s)
One or more input rod files

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

List[RodBinding[Feature]]  []

--showSkipped / -s

If true, this tool will print out the skipped locations

boolean  false

--verbose / -v

If true, this tool will print out detailed information about the rods it finds and locations

boolean  false

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