Outputs a list of intervals that are covered to or above a given threshold
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.
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.
One or more BAM files.
List of covered (or uncovered) intervals.
java -jar GenomeAnalysisTK.jar \ -T FindCoveredIntervals \ -R reference.fasta \ -I my_file.bam \ [-cov 10 \] [-uncovered \] -o output.list
These Read Filters are automatically applied to the data by the Engine before processing by FindCoveredIntervals.
This tool applies the following downsampling settings by default.
This tool uses ActiveRegions on the reference.
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.
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 | |||
| --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 | |
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.
Threshold for the probability of a profile state being active.
Double 0.002 [ [ 0 1 ] ]
The active region extension; if not provided defaults to Walker annotated default
Integer NA
Use this interval list file as the active regions to process
List[IntervalBinding[Feature]] NA
The active region maximum size; if not provided defaults to Walker annotated default
Integer NA
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
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
The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default
Double NA
The minimum allowable coverage to be considered covered
int 20 [ [ -∞ ∞ ] ]
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
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 [ [ -∞ ∞ ] ]
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 [ [ -∞ ∞ ] ]
The minimum allowable base quality score to be counted for coverage
int 0 [ [ -∞ ∞ ] ]
The minimum allowable mapping quality score to be counted for coverage
int 0 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout
output intervals that fail the coverage threshold instead
boolean false