Realigner Target Creator

Good day.
Has anyone ever come across the following ERROR message: Please note that I have just edited the file name and pathway in order to post this query.

INFO 14:36:18,224 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR A USER ERROR has occurred (version 2.4-9-g532efad):
ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
ERROR Please do not post this error to the GATK forum
ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: SAM/BAM file SAMFileReader{/pathway_to_/file_name.sorted.dedup.bam} appears to be using the wrong encoding for quality scores: we encountered an extremely high quality score of 62; please see the GATK --help documentation for options related to this error

Is there any documentation that will show me how to deal with this specific problem?
I thank you in advance


Best Answer


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