Dr. Mc. Ninja
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Recent activity by Dr. Mc. Ninja
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Short version (please let me know if it works): Short Answer / FixThis error happens because the compute environment you're using does not have the VEP Docker image installed, so Hail tries to run:...
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Short answerThe “helper” tables that UK Biobank distribute with the WES VCFs intentionally keep only the minimal ANN/ CSQ columns that are needed for most high-level filtering. UKB ran snpEff v5 wi...
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Here is what my assistant came up with as an answer for this question… Please take all the ‘statements’ with a pinch of salt. YMMV as they say ;-)Cheers,Below is a practical “recipe” that UK Bioban...
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- 2 votes
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My assistant said… This is a classic SAIGE “you asked for LOCO but didn’t bake LOCO into the cake” situation 🍰🧬 You ran Step 1 (null model / GRM) without LOCO, but Step 2 is trying to use LOCO. St...
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No problem, happy to share the full sheet if it's useful (I guess I may as well): rap_instance_type,aws_instance_type,version,storage_class,storage_rank,gpus,memory_class,vcpus,memory_gib,storage_g...
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- 1 vote
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Thanks so much. Here is a visualisation that's useful for me:
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What’s tripping you up is this:Table Exporter doesn’t “export files from your project”. It exports columns from the dispensed UKB Dataset / Cohort / Dashboard into a new CSV/TSV. The only role your...
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Short answer: yes, that’s correct 👍On the UK Biobank RAP (DNAnexus), you are only charged once a job actually starts running on an instance. Jobs that exceed the concurrent running limit (for examp...
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My assistant says … (NOTE, she has the habit of optimistically making stuff up, so please let me know if this works or not) …You’re not doing anything “wrong” – this is mostly about how Hail + Spar...
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My assistant came up with the below. Sorry cus the formatting is a bit off, and I haven't tested it. What’s actually going wrong?This bit tells the whole story:Unable to find image dnanexus/dxjupyt...
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