Y R
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Latest activity by Y R-
Y R commented,
So from what I understand of it for exome data we need to use our own references? The references on the cloud are only for genome data? Gökalp Çelik
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Y R commented,
This is where I start getting confused (plus an explanation of what confuses me): 1) The first link you mentioned (https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle )...
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Y R commented,
I mean the reference fasta, interval lists, etc. anything that could be used for GATKgCNV given that it can have issues with mitochondrial regions as well as other regions.
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Y R created a post,
GATKgCNV References For Hg19 and Hg38
I cannot seem to find the recommended references by GATKgCNV for hg19 and hg38. I have used it before but I cannot find it currently. If this question is not allowed I can take it down. Does anyone...
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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) ...