DepthOfCoverage: Error with option -baseCounts

pMehannapMehanna Member
edited January 23 in Ask the GATK team
Hi all!

I'm trying to use DepthOfCoverage with this command:
java -jar home/apps/Logiciels/GATK/3.6-0/GenomeAnalysisTK.jar -l INFO -T DepthOfCoverage -R ref.fasta -I input.bam -L intervals.bed -baseCounts true -o output_DoC

and it keeps giving me this error:
##### ERROR MESSAGE: Invalid argument value 'true' at position 11.

I'm using version 3.6 of GATK and java jdk1.8.0_40.

Thank you,

Best Answer

  • bshifawbshifaw moon admin
    edited January 23 Accepted Answer

    @pMehanna ,

    GATK is erroring out because of the "true" in your command. Having the option -baseCountsin the command should be sufficient enough to "Add base counts to per-locus output", no need to add true afterwards.


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