Walks over the input data set, calculating the number of bases seen for diagnostic purposes.
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]
This Read Filter is automatically applied to the data by the Engine before processing by CountBases.
This tool does not apply any downsampling by default.
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).
GATK version 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.