Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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My idea I am seeing "stream: true" in the parameter_meta spec for input files. Mounting/Streaming files is typically done via dxfuse, and that is indeed a Read-only file system. In the mv etc. oper...
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Good to know, thanks. So if it is a bed file, could you run your bcftools without it? as a testing run?
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Instead of ...$dnanexus_link"...: A) what if you specify it like here: https://github.com/dnanexus/dxCompiler/blob/develop/contrib/beginner_example/bam_chrom_counter_input.json ? https://github.com...
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OK, so I think that the issue is related to the file-GPXPz48JG7JFb0V0q10kYzXz itself. It seems to me that the file (is this file included in the exported vfcs list?) cannot be downloaded/accessed.
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For docker, I prefer saving it first to tar and use the following option:https://github.com/dnanexus/dxCompiler/blob/develop/doc/ExpertOptions.md#storing-a-docker-image-as-a-file In this specific c...
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I think you could use standard bioinformatics tools such as PLINK (to extract genotype data and filter) and then use another bioinformatics tool to merge the data. https://www.biostars.org/p/422771...
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The query of the week #2 is primarily focusing on writing an advanced query in SQL. I consider Imaging data just as an interesting application, but the SQL approach could be reused somewhere else.
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Hi @Jeremy Chang?, I would be interested in knowing if the Hail error messages would be captured by the Spark UI: https://documentation.dnanexus.com/developer/apps/developing-spark-apps#monitoring...
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If my understanding is correct, it would be essential to define "cohort of unrelated individuals". With that, one could then write a query in Python/R Jupyter to retrieve that data (eids). https://...
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Thanks for the update!
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