Prints out counts of the number of reference ordered data objects encountered along the reference.
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
These Read Filters are automatically applied to the data by the Engine before processing by CountRODsByRef.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--rod||List[RodBinding[Feature]]||||Input VCF file(s)|
|--showSkipped||boolean||false||If true, this tool will print out the skipped locations|
|--verbose||boolean||false||If true, this tool will print out detailed information about the rods it finds and locations|
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.
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
If true, this tool will print out the skipped locations.
If true, this tool will print out detailed information about the rods it finds and locations.
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.