FindCoveredIntervals

Outputs a list of intervals that are covered to or above a given threshold

Category Diagnostics and Quality Control Tools

Traversal ActiveRegionWalker

PartitionBy CONTIG


Overview

The output list can be used as an interval list for other tools. The logic can be inverted using the -uncovered argument argument to instead output intervals that fail the coverage threshold.

Application example: find and diagnose low-coverage regions

Run this toool first with the -uncovered argument to identify regions that have low coverage. Then run DiagnoseTargets on the output intervals to diagnose why they are poorly covered.

Input

One or more BAM files.

Output

List of covered (or uncovered) intervals.

Example

 java -jar GenomeAnalysisTK.jar \
   -T FindCoveredIntervals \
   -R reference.fasta \
   -I my_file.bam \
   [-cov 10 \]
   [-minBQ 20 \]
   [-minMQ 20 \]
   [-uncovered \]
   -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

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.

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
0 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
--activeProbabilityThreshold
 -ActProbThresh
0.002 Threshold for the probability of a profile state being active.
--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
--maxReadsInMemoryPerSample
30000 Maximum reads per sample given to traversal map() function
--maxTotalReadsInMemory
10000000 Maximum total reads given to traversal map() function
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.


--activeProbabilityThreshold / -ActProbThresh

Threshold for the probability of a profile state being active.

Double  0.002  [ [ 0  1 ] ]


--activeRegionExtension / -activeRegionExtension

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

Integer  NA


--activeRegionIn / -AR

Use this interval list file as the active regions to process

List[IntervalBinding[Feature]]  NA


--activeRegionMaxSize / -activeRegionMaxSize

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

Integer  NA


--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  NA


--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  NA


--bandPassSigma / -bandPassSigma

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

Double  NA


--coverage_threshold / -cov

The minimum allowable coverage to be considered covered

int  0  [ [ -∞  ∞ ] ]


--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


--maxReadsInMemoryPerSample / -maxReadsInMemoryPerSample

Maximum reads per sample given to traversal map() function
What is the maximum number of reads we're willing to hold in memory per sample during the traversal? This limits our exposure to unusually large amounts of coverage in the engine.

int  30000  [ [ -∞  ∞ ] ]


--maxTotalReadsInMemory / -maxTotalReadsInMemory

Maximum total reads given to traversal map() function
What is the maximum number of reads we're willing to hold in memory per sample during the traversal? This limits our exposure to unusually large amounts of coverage in the engine.

int  10000000  [ [ -∞  ∞ ] ]


--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


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