Count the number of reads
This is especially useful in combination with read filters (see the --read-filter command line argument) which allow you to count reads matching specific criteria (e.g. read group tags or quality parameters).
One or more BAM files.
Number of reads seen. This is output to the terminal/stdout.
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T CountReads \ -I input.bam \ [-L input.intervals]
These Read Filters are automatically applied to the data by the Engine before processing by CountReads.
This tool can be run in multi-threaded mode using this option.
This tool does not apply any downsampling by default.
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.
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.