Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Awesome!
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I checked that using file (https://en.wikipedia.org/wiki/File_(command)) command executed inside ttyd workstation: file "/mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, pVCF...
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From the lines in your error log, "Downloading files using 4 threads+ [[ '' == '' ]]+ eval 'amtools view -T GRCh38_full_analysis_set_plus_decoy_hla.fa -b 6000001_23143_0_0.cram > output.bam'++ amto...
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Hi @Burcu Çevik?, one line in the job log you shared says"downloading file: file-G55jg28JykJfF2KJ4yPQFz40 to filesystem: /home/dnanexus/in/in/1/1000229_23143_0_0.cram.crai". It appears you provided...
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To convert cram to bam, you will need cram and reference file. I did an example testing run via SAK GUI on the "/Bulk/Exome sequences/Exome OQFE CRAM files/": A) I clicked on Input files and select...
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UKB phenotypic data is stored in the form of Dataset. This can be then quickly queried using Spark / Spark SQL / dxdata Python package. I would start with the following links: https://dnanexus.gitb...
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If I am correct, all the new files that were created in temporary folder are copied back to the parent dnax project as outputs from SAK. Normally, files are copied/saved to root folder of your proj...
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UKB-RAP platform does not have this software at this moment. As an alternative, you might explore possibilities for working with similar plots and viewers in JupyterLab/R, JupyterLab/python. e.g. h...
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I do not think there is an official version of that tool in SAK. I was able to locate the same version as you mentioned - RAP (v4.6.0) includes an older version of plink2 (v2.00a2.3LM). I went ahea...
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Swiss Army Knife 4.7.0 has been released.
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