Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Interesting, perhaps this would depend on which JupyterLab flavor you choose.
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In the past, when I worked with VCF annotation tools, I used GEMINI a lot: https://gemini.readthedocs.io/en/latest/It is a framework collecting many variant annotation tools and also it has a nice ...
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Downloading/Accessing a different DB for SNPeff would be a good idea.
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Hello @Diana Cornejo?, some possibilities for using bash and interacting with data are elaborated here: https://community.dnanexus.com/s/question/0D5t000004SDdTCCA1/query-of-the-week-3-bring-your-c...
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This looks like a current limitation of the Cohort Browser Tile vis. I use CB more as a tool to quickly Preview data and get some insight about data distribution. I suggest running JupyterLab and p...
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Thanks, OK, the job has not been restarted. I am sharing more ideas. As per dxcompiler ExpertOptions documentation - https://github.com/dnanexus/dxCompiler/blob/develop/doc/ExpertOptions.md#setting...
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If you do dx describe job-GP3ybZQJg8Jkpj3z5GQyf91v, how many failureCounts do you see?
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I think that the codebase for Coffee Break is not published publicly. However, for your code availability and extract phenotype data questions, there is a bunch of newer and updated materials docu...
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My understanding is that e.g. test/mydata.tsv.gz is saved into HDFS file system (Cluster distributed hadoop storage). You could try to move it from hdfs to Local notebook storage (/opt/...) using "...
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Does your in-house pipeline (non-RAP) use Spark? If so, which library/method?
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