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dnanexus / UKB_RAP

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.
MIT License
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Update partD-step1-regenie.sh #18

Closed kmcgurk closed 1 year ago

kmcgurk commented 1 year ago

Hey Anastazie,

Really love the code you have provided and your DNA Nexus tutorials!

I've noticed an issue to the GWAS code partD-step1-regenie.sh: I think this line: -icmd=${run_plink_wes} should read: -icmd="${run_regenie_step1}"

Also I noticed you added ";" at the end of the chunks of code for part D only - they're not in the other parts, maybe they don't have an effect but I haven't added them just in case!

Thanks,

Kathryn

anastazie-dnanexus commented 1 year ago

Dear Kathryn, Thank you for catching this and sorry for the late reply.

Cheers, Anastazie

kmcgurk commented 1 year ago

No problem!

Thanks for all of your tutorials and open access code!

Kathryn

Dr. Kathryn McGurk BHF Immediate PBSR Fellow National Heart and Lung Institute Imperial College London Twitter & LinkedIn: @KathrynMcGurk

From: Anastazie Sedlakova @.> Date: Thursday, 20 April 2023 at 12:37 To: dnanexus/UKB_RAP @.> Cc: McGurk, Kathryn A @.>, Author @.> Subject: Re: [dnanexus/UKB_RAP] Update partD-step1-regenie.sh (PR #18) This email from @.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders listhttps://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address.

Dear Kathryn, Thank you for catching this and sorry for the late reply.

Cheers, Anastazie

— Reply to this email directly, view it on GitHubhttps://github.com/dnanexus/UKB_RAP/pull/18#issuecomment-1516177906, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AOHDWZBX4PAJHG5PXKSZNALXCENVZANCNFSM6AAAAAAUBXCED4. You are receiving this because you authored the thread.Message ID: @.***>