Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
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]
This Read Filter is automatically applied to the data by the Engine before processing by CountReads.
This tool can be run in multi-threaded mode using this option.
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 2.5-2-gdb4546e built at 2013/05/01 09:32:36.