Jose Aragon
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Latest activity by Jose Aragon-
Jose Aragon commented,
In the "Usage examples" and the "To additionally bin base qualities" section in this page the argument tool: --reference -R is missing.
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Jose Aragon commented,
I checked for any typo and I cannot see anything that can be related to spaces or other type of typos. I tried another computer and here is the command line: gatk ApplyBQSR \--java-options "-Xmx48G...
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Jose Aragon commented,
Thank you for your response. Yes, I checked this post. It is not solving my problem. My code has no spaces in the tags: Bad tag: - R Good tag: -R Could it be that it is from a different tool? In ...
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Jose Aragon created a post,
ApplyBQSR no positional argument is defined for this tool
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.2.0.0b) Exact command used: gatk ApplyBQSR \--java-options "-Xmx14G" \–R GRCh38.dna.primary_assembly/GRCh38.dna.primar...