GATK question

[milesgr]

This is probably a simple question, but I aligned several files using BWA, I then merged the BAM files and sorted them using samtools. I am now trying to run GATK using a simple CountReads function. The command I ran:

java -jar GenomeAnalysisTK.jar -T CountReads -R /data/genomes/H_sapiens/hg19/hg19.fa /path_to_bam/S_merged.bam

I get the below error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.5-2-g5200f7f):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid argument value '/data/results/milesgr/LFS_TWIN_S/S_merged.bam' at position 4.
##### ERROR ------------------------------------------------------------------------------------------


Any thoughts as to what may be going wrong?

[behavin]

Well you're leaving out the -I before your bam location.