I am trying to run joint-discovery workflow, but I am getting this error : A USER ERROR has occurred: use-new-qual-calculator is not a recognized option, when I am using broadinstitute/gatk:22.214.171.124 and this :A USER ERROR has occurred: Bad input: Presence of '-RAW_MQ' annotation is detected. This GATK version expects key RAW_MQandDP with a tuple of sum of squared MQ values and total reads over variant genotypes as the value. This could indicate that the provided input was produced with an older version of GATK. Use the argument '--allow-old-rms-mapping-quality-annotation-data' to override and attempt the deprecated MQ calculation. There may be differences in how newer GATK versions calculate DP and MQ that may result in worse MQ results, when I am trying to use the latest gatk version. Can anyone help me?
Thank you in advance!
Please sign in to leave a comment.