Gabriel Doctor

Thanks this is a reasonable answer

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• 16 May 2025 10:46
• 0 votes

Hi Sebastian, i wrote this applet to allow an easy way of accessing UKB RAP data from the command line, with interactive and submit modes.https://github.com/gtdoctor/BasicBashWorker_for_UKBiobankDN...

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• 02 May 2025 13:25
• 1 vote

Speed/throttling when submitting 1000s of jobs

HiPlease could you let me know if there is any constraint against queing up e.g. 1000 or 2000 jobs to be done as  lowpriority workers become available? the jobs are accessing a few small similar fi...

• Gabriel Doctor
• 21 March 2025 16:42
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Hi HannahIf you haven't checked whether the instance size is large enough that's probably a good place to start; and check paths etc on your script.  But if you're anything like me, i get frequentl...

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• 30 January 2025 13:30
• 2 votes

Optimising speed of extracting specific loci from WGS

I am trying to get info from c500,000 loci scattered throughout genome (basically allele freqs of whole UK pop at specific sites). That means that I need to access thousands of VCF for chunked regi...

• Gabriel Doctor
• Edited 26 November 2024 10:46
• 2 followers
• 1 comment
• 0 votes

It would be a small file with 3 columns! ID, position_GRCH37, position_GRCH38, approx 800k rows.  Simple to update a plink.bim file with this and much cheaper for users than the liftover pipeline  

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• 27 September 2024 17:10
• 0 votes