CountRODs

Prints out counts of the number of reference ordered data objects encountered.

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

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).

Input

One or more rod files.

Output

Number of rods seen.

Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -T CountRODs \
   -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 CountRODs.

Parallelism options

This tool can be run in multi-threaded mode using these options.

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).

CommandLineGATK

CountRODs specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists
--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

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.

--out / -o ( PrintStream with default value stdout )

An output file created by the walker. Will overwrite contents if file exists.

--rod / -rod ( List[RodBinding[Feature]] with default value [] )

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

--showSkipped / -s ( boolean with default value false )

If true, this tool will print out the skipped locations.

--verbose / -v ( boolean with default value false )

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.