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CountBases -o option

tommycarstensentommycarstensen United KingdomMember ✭✭✭

I wanted to calculate the depth of coverage of my bam and as part of that calculation did this:
java -Xmx200m \
-jar GATK.jar \
-T CountBases \
-o CountBases.out \
-I $mybam \

However, I got this error:

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.1-13-g0f021e6):
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 See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR MESSAGE: Argument with name 'o' isn't defined.
ERROR ------------------------------------------------------------------------------------------

-o is allowed according to http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_qc_CountBases.html

Is this the right place to submit bugs?

A feature request:
PrintReads has a --downsample_coverage option. This allows me to downsample by a given ratio. It would be great, if I could also downsample to a given depth of coverage with this tool without having to calculate the depth of coverage a priori.

Best Answer


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