Walks over the input data set, calculating the number of bases seen for diagnostic purposes.

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ



One or more BAM files.


Number of bases seen.


 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CountBases \
   -I input.bam \
   [-L input.intervals]

Additional Information

Read filters

This Read Filter is 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

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).

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GATK version 3.3-0-g37228af built at 2014/10/24 14:40:51. GTD: NA