CountReadEvents

Count the number of read events

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


Overview

This tool counts the number of "events" (I, D, M etc) encountered in the CIGAR strings of the sequence reads.

Input

One or more BAM files.

Output

Number of read events for each category, formatted as a GATKReport table.

Usage example

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

Additional Information

Read filters

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

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.

CountReadEvents 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
--out
 -o
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 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.