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I had to Google it, but found it: https://gatkforums.broadinstitute.org/gatk/discussion/8692/version-highlights-for-gatk-version-3-7 And I look crazy talking to myself!
Funny... I've tried using the short version of the "--standard" commands and now I get a different error: ERROR MESSAGE: Invalid command line: The parameter standard_min_confidence_threshold_for_emitting is deprecated: This argument is no…
I have noticed that when I remove the --standard_min_confidence_threshold_for_calling/emitting, the script works fine. What is about those commands that HC does not recognize the -ERC command?
Hi, I am having a similar issue as the one above. I am trying to run HaplotypeCaller from GATK v.3.8, and I am getting the following error: Invalid argument value '-ERC GVCF' I have tried using '-emitRefConfidence GVCF', and also adding the option…
Hello there! I am also getting a similar error, though I don't know how to fix it. I got the VCF file from a collaborator and I'm running with a reference that I downloaded and indexed, but they are supposed to be exactly the same reference. Ex…