Kristen

Bulk-downloading job logs and investigating failed jobs

Getting logs for many jobs at onceHere are some commands that can help you fetch your job logs in bulk and write each one to a separate file for easy searching/grepping:# Make a list of jobs to get...

• Kristen
• Edited 28 August 2025 03:18
• 1 follower
• 0 comments
• 0 votes

How to use Swiss Army Knife for an interactive/ssh session

Although Swiss Army Knife is designed for non-interactive use, there are times when it is helpful to be able to use it interactively.To get an interactive session, have Swiss Army Knife run the “sl...

• Kristen
• Edited 05 September 2025 21:40
• 1 follower
• 0 comments
• 4 votes

Getting dx fuse (/mnt/project/) and the dx upload/download commands to work on Cloud Workstation

Cloud Workstation is great for those of us who like to work over ssh instead of using a web browser, but it can require a little extra setup to get access to files in the project space working.Gett...

• Kristen
• 28 August 2025 02:11
• 1 follower
• 0 comments
• 4 votes

There is a plink version of the 500k WGS data available now in pgen format.  If it makes sense, maybe migrate the analyses from the imputed data to the WGS plink datasets. Good suggestion, but thos...

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• 25 August 2025 17:49
• 0 votes

Caveat to the above: When I say that Plink or most analysis tools will still produce correct allele frequencies, effect estimates, etc. I mean tools that use one data source for the whole process. ...

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• Edited 15 August 2025 04:20
• 2 votes

Here are results to confirm what Ahmet reported, the DRAGEN .bgen files are ref-last.Using the following test SNPs on chromosome 21, I compared different versions of the genotype data:rsid ...

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• Edited 15 August 2025 04:18
• 2 votes

It's still there for me: /Bulk/Genotype Results/Genotype calls/ukb_rel.datHere are some things to check if you can't see it: Make sure you have the array genotyping data dispensed to your project. ...

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• Edited 14 August 2025 20:45
• 1 vote

Could we have a Community section for sharing "tips and tricks"?

As people are making the move to UKB RAP, sometimes we figure out a tip or trick we want to share.Right now most of the sections of the Community forum are mostly questions - could we have a sectio...

• Kristen
• 14 August 2025 20:35
• 2 followers
• 1 comment
• 0 votes

I second this suggestion.Plink is one of the most widely used genetics tools out there, and Plink's .bed format is widely supported by other genetics tools as well. Only making the data available i...

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• 14 August 2025 20:25
• 3 votes