Count the number of ROD 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 -jar GenomeAnalysisTK.jar \ -T CountRODsByRef \ -R reference.fasta \ -o output.txt \ --rod input.vcf
These Read Filters are automatically applied to the data by the Engine before processing by CountRODsByRef.
This tool applies the following downsampling settings by default.
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.
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 | |||
| --rod |
[] | Input VCF file(s) | |
| Optional Flags | |||
| --showSkipped -s |
false | If true, this tool will print out the skipped locations | |
| --verbose -v |
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
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]] []
If true, this tool will print out the skipped locations
boolean false
If true, this tool will print out detailed information about the rods it finds and locations
boolean false