Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Hi @Royce Clifford?, it has been a long time since the last activity on this thread. Please create a new post and reference this one. It will have a better visibility for others, so they could cont...
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If the 273K females are included in the pVCF that is available to researchers, then I would start with that. If not, then it might be required for you to use GLnexus.
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Why do you think it is putting "--max-alleles 20" to "--max-alleles 2"? Is this information explicitly available in the job log? One more question, if the two VCFtools commands (on UKB RAP vs. outs...
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How does your Swiss Army Knife VCFtools command look like? Is this exactly the same command you use outside of DNAnexus?
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This worked for me: Specified a genotype filter, i.e. rsid. Clicked on Data Preview tab. Inspected the filtered Participant IDs (samples / eids). Could export sample ids directly to csv OR Saved r...
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Hi @Saurabh Mishra?, for those who are coming from high performance computing, there was a webinar to learn about equivalent cloud-based methods for running bioinformatics jobs quickly on the Rese...
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Hi @Pierre LIndenbaum?, For using " Directory" type, make sure that the WDL script uses version development (I am not sure if it is also in 1.1) Directory type input needs to be in the DNAnexus U...
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You would access OMOP the same way as other phenotypic data (Spark, dxdata, "dx extract_dataset", or Table Exporter). https://dnanexus.gitbook.io/uk-biobank-rap/working-on-the-research-analysis-pla...
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That is interesting! For ICD10 in UKB RAP, I normally use Cohort Browser to see the mapping between code and diagnosis group. Sometimes, I find a publicly available ICD10 code mapping useful, e.g. ...
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Also I can imagine the situation when I run JupyterLab Terminal and execute "dx run swiss-army-knife" from there. This will produce the results noninteractively, so I can later use it in my downst...
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