Prints out counts of the number of reference ordered data 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.


 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -T CountRODsByRef \
   -R ref.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

Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

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

--rod binds reference ordered data. This argument supports ROD files of the following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, 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

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA