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

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


Can also count the number of reads matching a given criterion using read filters (see the --read-filter command line argument). Simplest example of a read-backed analysis.


One or more BAM files.


Number of reads seen.


 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -R ref.fasta \
   -T CountReads \
   -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 CountReads.

Parallelism options

This tool can be run in multi-threaded mode using this option.

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).

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA