FindCoveredIntervals

Category Diagnostics and Quality Control Tools

Traversal ActiveRegionWalker

PartitionBy CONTIG

Introduction

Additional Information

Read filters

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

ActiveRegion settings

This tool uses ActiveRegions on the reference.

Minimum region size: 50 bp
Maximum region size: 50,000 bp
Extension increments: 0 bp

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

FindCoveredIntervals 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
Required
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists
Optional
--activeRegionIn	List[IntervalBinding[Feature]]	NA	Use this interval list file as the active regions to process
--activeRegionOut	PrintStream	NA	Output the active region to this IGV formatted file
--activityProfileOut	PrintStream	NA	Output the raw activity profile results in IGV format
--coverage_threshold	int	20	The minimum allowable coverage to be considered covered
--uncovered	boolean	false	output intervals that fail the coverage threshold instead
Advanced
--activeRegionExtension	Integer	NA	The active region extension; if not provided defaults to Walker annotated default
--activeRegionMaxSize	Integer	NA	The active region maximum size; if not provided defaults to Walker annotated default
--bandPassSigma	Double	NA	The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default

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.

--activeRegionExtension / -activeRegionExtension ( Integer )

The active region extension; if not provided defaults to Walker annotated default.

--activeRegionIn / -AR ( List[IntervalBinding[Feature]] )

Use this interval list file as the active regions to process.

--activeRegionMaxSize / -activeRegionMaxSize ( Integer )

The active region maximum size; if not provided defaults to Walker annotated default.

--activeRegionOut / -ARO ( PrintStream )

Output the active region to this IGV formatted file. If provided, this walker will write out its active and inactive regions to this file in the IGV formatted TAB deliminated output: http://www.broadinstitute.org/software/igv/IGV Intended to make debugging the active region calculations easier

--activityProfileOut / -APO ( PrintStream )

Output the raw activity profile results in IGV format. If provided, this walker will write out its activity profile (per bp probabilities of being active) to this file in the IGV formatted TAB deliminated output: http://www.broadinstitute.org/software/igv/IGV Intended to make debugging the activity profile calculations easier

--bandPassSigma / -bandPassSigma ( Double )

The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default.

--coverage_threshold / -cov ( int with default value 20 )

The minimum allowable coverage to be considered covered.

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

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

--uncovered / -u ( boolean with default value false )

output intervals that fail the coverage threshold instead.

GATK version 2.4-9-ge182083 built at 2013/03/19 07:40:48.