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Count the number of reads ending in insertions, deletions or soft-clips

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


This tool reports the number of reads where the end bases do not map to the reference sequence.


One or more BAM files.


Number of reads ending in each category.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -T CountTerminusEvent \
   -R reference.fasta \
   -I input.bam \
   -o output.txt \
   [-L input.intervals]

Additional Information

Read filters

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

Downsampling settings

This tool does not apply any downsampling by default.

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.

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

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.

--out / -o

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

PrintStream  stdout

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.