Y R
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Latest activity by Y R-
Y R commented,
I was just curious. Thank you Gökalp Çelik.
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Y R commented,
I ran it with about 200 samples I got what looks like the same error : 18:30:48.256 INFO GermlineCNVCaller - Shutting down engine [November 26, 2023 at 6:30:48 PM GMT] org.broadinstitute.hellbende...
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Y R commented,
Gökalp Çelik Therefore that is the best option for a script that has already been debugged to suppress the warning messages? Is there anything else you would suggest?
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Y R commented,
Gökalp Çelik If I set the verbosity to `--verbosity ERROR` will it only show the errors or will it show everything but the errors? Would this suppress the warnings I am getting? Or should I do some...
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Y R commented,
Thank you. Is there a way to suppress warnings unless it is an error?
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Y R created a post,
JexlEngine - ![0,14]: 'ReadPosRankSum < -20.0;' undefined variable ReadPosRankSum For GATK VariantFiltration
I am not sure if this question is allowed but I am having a bit of difficulty using the Variant Filtration command and I cannot seem to find a way around it. REQUIRED for all errors and issues: a) ...
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Y R commented,
Incorporation Of Suggestion: It worked. Thank you. Current Error: 5:24:14.722 INFO GermlineCNVCaller - Shutting down engine[November 15, 2023 at 3:24:14 PM GMT] org.broadinstitute.hellbende...
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Y R commented,
I am not sure I fully understand but I can do a `wc -l` for each interval and check the `tail` ends here: Step 1: Preprocess Intervals Word Count: `wc -l` produces 781866 The tail: chr21 48081660...
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Y R commented,
Regarding the previous suggestion: Thank you for your suggestion. Your suggestion worked for the error. Basic Information And Statement Of Problem: I am currently test driving the script on 5 te...
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Y R commented,
Hello Gökalp Celik, I used the references recommended by GATK for hg19 and then I got a peculiar error dealing with the contig ploidy priors table: The following mandatory columns could not be ...