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We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
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Tool in GATK to gather BQSR reports

nilsfulcrumnilsfulcrum Boston MAMember

I would like to request a feature from the GATK developers to be included in the toolkit. To parallelize BQSR, it is necessary to merge the GATK BQSR reports. I found the following post from a few years ago stating that the tool to gather BQSR reports would be out shortly: http://gatkforums.broadinstitute.org/gatk/discussion/1919/parallelizing-base-quality-score-recalibration

Could you please add this tool to GATK? Not all folks use Queue, and it seems like this is generally useful when trying to parallelize BQSR on large datasets to make it complete in a reasonable amount of time. Given the main method is only a few lines of code, a GATK developer should be able to get this done very quickly.



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