CountIntervals

Count contiguous regions in an interval list

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


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.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T CountIntervals \
   -R reference.fasta \
   -o output.txt \
   -check intervals.list
 

Additional Information

Read filters

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

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.

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
[] 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

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

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, 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  2  [ [ -∞  ∞ ] ]


--out / -o

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

PrintStream  stdout


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