Count contiguous regions in an interval list
When the GATK reads in intervals from an intervals list, any intervals that overlap each other get merged into a single interval spanning the original ones. For example, if you have the following intervals:
One or more ROD files containing intervals to check.
Number of separate intervals identified by GATK after merging overlapping intervals.
You can use the -numOverlaps argument to find out how many cases you have of a specific number of overlaps.java -jar GenomeAnalysisTK.jar \ -T CountIntervals \ -R reference.fasta \ -o output.txt \ -check intervals.list
These Read Filters are automatically applied to the data by the Engine before processing by CountIntervals.
This tool applies the following downsampling settings by default.
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 Inputs | |||
| --check |
[] | Any number of RODs | |
| Optional Outputs | |||
| --out -o |
stdout | An output file created by the walker. Will overwrite contents if file exists | |
| Optional Parameters | |||
| --numOverlaps -no |
2 | Count all occurrences of X or more overlapping intervals; defaults to 2 | |
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.
Any number of RODs
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3
List[RodBinding[Feature]] []
Count all occurrences of X or more overlapping intervals; defaults to 2
int 2 [ [ -∞ ∞ ] ]
An output file created by the walker. Will overwrite contents if file exists
PrintStream stdout