Count the number of bases in a set of reads
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.
java -jar GenomeAnalysisTK.jar \ -R reference.fasta \ -T CountBases \ -I input.bam \ [-L input.intervals]
These Read Filters are automatically applied to the data by the Engine before processing by CountBases.
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.