FindCoveredIntervals

Outputs a list of intervals that are covered above a given threshold.

Category Diagnostics and Quality Control Tools

Traversal ActiveRegionWalker

PartitionBy CONTIG


Overview

The list can be used as an interval list for other walkers. Note that if the -uncovered argument is given, the tool will instead output intervals that fail the coverage threshold.

Input

One or more BAM files.

Output

List of covered (or uncovered) intervals.

Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -T FindCoveredIntervals \
   -R ref.fasta \
   -I my_file.bam \
   -o output.list
 

Additional Information

Read filters

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

Downsampling settings

This tool applies the following downsampling settings by default.

  • Mode: BY_SAMPLE
  • To coverage: 1,000

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).

FindCoveredIntervals 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
Optional Outputs
--activeRegionOut
 -ARO
NA Output the active region to this IGV formatted file
--activityProfileOut
 -APO
NA Output the raw activity profile results in IGV format
--out
 -o
stdout An output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--coverage_threshold
 -cov
20 The minimum allowable coverage to be considered covered
--minBaseQuality
 -minBQ
0 The minimum allowable base quality score to be counted for coverage
--minMappingQuality
 -minMQ
0 The minimum allowable mapping quality score to be counted for coverage
Optional Flags
--uncovered
 -u
false output intervals that fail the coverage threshold instead
Advanced Inputs
--activeRegionIn
 -AR
NA Use this interval list file as the active regions to process
Advanced Parameters
--activeRegionExtension
NA The active region extension; if not provided defaults to Walker annotated default
--activeRegionMaxSize
NA The active region maximum size; if not provided defaults to Walker annotated default
--bandPassSigma
NA The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default
Advanced Flags
--forceActive
false If provided, all bases will be tagged as active

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

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

Integer


--activeRegionIn / -AR

Use this interval list file as the active regions to process

List[IntervalBinding[Feature]]


--activeRegionMaxSize / -activeRegionMaxSize

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

Integer


--activeRegionOut / -ARO

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

PrintStream


--activityProfileOut / -APO

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

PrintStream


--bandPassSigma / -bandPassSigma

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

Double


--coverage_threshold / -cov

The minimum allowable coverage to be considered covered

int  20  [ [ -?  ? ] ]


--forceActive / -forceActive

If provided, all bases will be tagged as active
For the active region walker to treat all bases as active. Useful for debugging when you want to force something like the HaplotypeCaller to process a specific interval you provide the GATK

boolean  false


--minBaseQuality / -minBQ

The minimum allowable base quality score to be counted for coverage

int  0  [ [ -?  ? ] ]


--minMappingQuality / -minMQ

The minimum allowable mapping quality score to be counted for coverage

int  0  [ [ -?  ? ] ]


--out / -o

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

PrintStream  stdout


--uncovered / -u

output intervals that fail the coverage threshold instead

boolean  false


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA