Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Hi @Chinonso Odebeatu?, yes, correct. You will need an active UKB RAP account. I believe this all will be covered in the webinar training this Thursday.
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How often do you export phenotypes, is it one time operation for you?
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Are there any other ways you prefer to export pheno data?
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In bash applet, to enable mounting /mnt/project/.../, I think you will need to add dxfuse binary to the resources folder:https://documentation.dnanexus.com/developer/apps/bash#downloading-inputs-us...
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@Lucy Gunnell? , Spark based technology might be a good option for this use case. https://documentation.dnanexus.com/science/using-hail-to-analyze-genomic-data#filter-by-variant-ids
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I have some experience with running R PheWAS from within the JupyterLab. For now, for installation details and a brief PheWAS discussion, please see the following thread: https://community.dnanexus...
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To one of your questions, "Have others been able to successfully use $in_prefix and $in_name keywords with swiss army knife from the command line?", I was able to test $in_prefix in SAK successful...
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UPDATE: My colleague, Nicholas H., looked into this in more details and it looks like this could be indeed an issue with bcftools command. He tried to modify the CMD_STR until he was able to get a...
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@Yong Qian?,For reporting an issue with data, please forward this Community post to ukbiobank-support@dnanexus.com.
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If I feel that the starting time is too long, I usually try to run the same job with a different instance type (with comparable mem, cpu and storage). It looks like the waiting time depends on the ...
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