CountRods is a RODWalker, and so traverses the data by ROD. For example if the ROD passed to it is a VCF file, it will count the variants in the file.
Note that this tool is different from CountRodsByRef which is a RefWalker, and so traverses the data by position along the reference. CountRodsByRef can count 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).
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 CountRODs \ -R ref.fasta \ -o output.txt \ --rod input.vcf
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