gatk 4.4 PrintReads "BQSR is not a recognized option"

booby35booby35 canadaMember
edited May 2018 in Ask the GATK team

Hi there,

I'm trying to perform base recalibration using GATK 4.4 docker image but PrintReads is crashing with the following error: "BQSR is not a recognized option". I tried -bqsr, -BQSR, --bqsr and --BQSR, since the online documentation is outdated and the local doc does not mention any "bqsr" option, it is very unclear how to use that tool or even if it actually still exists in the latest version.

what am I missing to perform that step as described in the GATK best practices?

Best,

B.

Post edited by booby35 on

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