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Count the number of bases in a set of reads

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ



One or more BAM files.


Number of bases seen. If an output file name is provided, then the result will be written to that file. Otherwise it will be sent to standard console output.

Usage example

 java -jar GenomeAnalysisTK.jar \
   -R reference.fasta \
   -T CountBases \
   -I input.bam \
   [-L input.intervals]

Additional Information

Read filters

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

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.

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