PrintRODs

Print out all of the RODs in the input data set

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool reports what RODs (reference ordered data sets) are contained in a given input.


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by PrintRODs.


Command-line Arguments

Engine arguments

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.

PrintRODs 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
Required Inputs
--input
NA The input ROD which should be printed out.
Optional Outputs
--out
 -o
stdout An output file created by the walker. Will overwrite contents if file exists

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.


--input / -input

The input ROD which should be printed out.

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

R RodBinding[Feature]  NA


--out / -o

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

PrintStream  stdout


Return to top


See also GATK Documentation Index | Tool Docs Index | Support Forum

GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.