Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Please report this to ukbiobank-support@dnanexus.com since they could get access to your log file and project. Would be nice to hear from you then what was the root cause :).
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OK, so then I would try to rerun with a larger instance type. Plus, Rstudio should be used in High priority mode.https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform...
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https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-platform/managing-job-priority#spot-vm-interruptions
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What might happen, in case it is a more computationally intensive job, it might consume all resources and got killed due to lack of memory. What did the error message say? You can try to change the...
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In order to get this info, I normally go to Cohort Browser and check details about each column, e.g.: It also contains a link to UKB Showcase, where this info is available as well. https://biobank....
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I believe you should be able to get this programatically with inspiration from this notebook:https://github.com/dnanexus/OpenBio/blob/master/dxdata/getting_started_with_dxdata.ipynb "Field - Repres...
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Could you please provide more illustrative example(s)? Screenshot, field id, gatk command...
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You can read specification of SnpEff tool.
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SnpEff is very versatile . Annotation and the resulting number of columns per row would depend on the selected annotation tool. In my experience, proper filtering is always needed to lower down the...
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So theoretically, given the fact that "output.vcf" is in root directory, one option would be to do something like df_vcf = read_vcf("/mnt/project/output.vcf")
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