# CountIntervals

Count contiguous regions in an interval list.

## Overview

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:

• 20:1-2000
• 20:1500-3000
They will be merged into a single interval:
• 20:1-3000
This tool allows you to check, for a given list of intervals, how many separate intervals the GATK will actually distinguish at runtime.

### Input

One or more rod files containing intervals to check.

### Output

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.

### Example

 java -Xmx2g -jar GenomeAnalysisTK.jar \
-T CountIntervals \
-R ref.fasta \
-0 output.txt \
-check intervals.list


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

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## 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).

### CountIntervals 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 Inputs
--check
NA Any number of RODs
Optional Outputs
--out
-o
NA 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

### 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.

### --check / -check

Any number of RODs

--check binds reference ordered data. This argument supports ROD files of the following types: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, OLDDBSNP, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

List[RodBinding[Feature]]

### --numOverlaps / -no

Count all occurrences of X or more overlapping intervals; defaults to 2

int  [ [ -∞  ∞ ] ]

### --out / -o

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

PrintStream