• April Ask Me Anything: Imaging Analysis

  • Brenton Pyle
  • 11 April 2022 00:00
  • 0 votes
  • 1 comment

• I want to locate the pVCF UKB23352_c19 file that has position chr19:17642033-17642056. There are 1000 files. How do I do it?

  • Former User of DNAx Community_10
  • 10 April 2022 00:00
  • 0 votes
  • 6 comments

• Hi, I am new to DNAnexus. I want to create a project. However, I met an error which is "The application is not enabled for RAP". I do have a UKB project and I enter the specific application ID. I wonder if you can help me? Thank you~

  • Former User of DNAx Community_83
  • 08 April 2022 00:00
  • 0 votes
  • 1 comment

• Is it expected that some WGS GraphTyper pVCF files have no variants?

  • Permanently deleted user
  • 07 April 2022 00:00
  • 0 votes
  • 6 comments

• How can I identify which subjects have which alleles of rs56041637 in the WGS data? rs56041637 is an intron variant not in the imputed snps. https://www.ncbi.nlm.nih.gov/snp/rs56041637

  • Former User of DNAx Community_10
  • 05 April 2022 00:00
  • 0 votes
  • 8 comments

• Why 0 participants but 416.36TiB of data?

  • Former User of DNAx Community_39
  • 04 April 2022 00:00
  • 0 votes
  • 6 comments

• Hi! If you're interested in dementia, check out the roundtable we just had https://www.youtube.com/watch?v=qwX4DN04g6w , and also this paper about meta-GWAS! https://www.nature.com/articles/s41588-022-01024-z

  • Ben Busby
  • 04 April 2022 00:00
  • 0 votes
  • 1 comment

• Copying workflows within projects and copying ICD codes in cohort browser.

  • Former User of DNAx Community_42
  • 01 April 2022 00:00
  • 0 votes
  • 3 comments

• I am a student researcher who is unsure about the financial impact of UKB RAP. Has anyone in a similar situation had any experience applying for enhanced credits and could share if it is easy to apply, and how to gauge if I'm likely to run out of credit?

  • Former User of DNAx Community_31
  • 01 April 2022 00:00
  • 0 votes
  • 3 comments

• How do I load .p.vcf.gz files into the python environment on the spark cluster? Do I need to use dxdata?

  • Former User of DNAx Community_4
  • 01 April 2022 00:00
  • 0 votes
  • 3 comments

• Hi, By whom and how were the helper filer for the 450K exomes generated? Has any filtering been applied for the pVCF or the plink files? Is the release on the RAP from this pipeline? https://www.nature.com/articles/s41586-021-04103-z

  • Former User of DNAx Community_79
  • 29 March 2022 00:00
  • 0 votes
  • 7 comments

• Is it possible to define a cohort using Cohort Browser that has a set of inpatient ICD9/ICD10 OR death ICD9/ICD10 codes? So far I am only able to define a cohort with a set of inpatient ICD9/ICD10 codes WITH death ICD9/ICD10 codes.

  • Former User of DNAx Community_46
  • 25 March 2022 00:00
  • 0 votes
  • 3 comments

• I am wondering where I can find joint calling for whole genome data. For whole exome data there are 3 folders (population level exome OQFE variants) with joint calls in plink, bgen and pvcf format, but I don't see similar folder under whole genome data?

  • Permanently deleted user
  • 24 March 2022 00:00
  • 0 votes
  • 3 comments

• What cost an almost finish job shifts to wait status and restart?

  • Permanently deleted user
  • 23 March 2022 00:00
  • 0 votes
  • 3 comments

• How to use Ensembl Variant Effect Predictor(VEP) on UKB data for GWAS?

  • Former User of DNAx Community_24
  • 23 March 2022 00:00
  • 0 votes
  • 1 comment

• Can I use GLnexus to create a pVCF for all of the females (273k people) in the UKB cohort?

  • Former User of DNAx Community_32
  • 22 March 2022 00:00
  • 0 votes
  • 4 comments

• Attempt to retrieve all data fields from a cohort failed in dxjupyter notebook. I am wondering what the error means and the best practice for retrieving all fields for every participant may be.

  • Former User of DNAx Community_26
  • 18 March 2022 00:00
  • 0 votes
  • 8 comments

• How to define a cohort from a list of EIDs?

  • Former User of DNAx Community_26
  • 18 March 2022 00:00
  • 0 votes
  • 4 comments

• Dear DNAnexsus team, Is it possible to turn the cohort browsers filters once a cohort has been generated into "code" for reproducibility/ more CLI orientated members of our team? Many thanks

  • Former User of DNAx Community_45
  • 17 March 2022 00:00
  • 0 votes
  • 5 comments

• Dementia Researcher Roundtable Mar 31: Working with Large-Scale Datasets to Enable Discovery

  • Brenton Pyle
  • 16 March 2022 00:00
  • 0 votes
  • 1 comment

• Webinar Apr 21: Image Analysis on the UK Biobank Research Analysis Platform

  • Brenton Pyle
  • 15 March 2022 00:00
  • 0 votes
  • 2 comments

• How can I run regenie step 2 for all 22 chromosomes at once? I would like regenie to spit out a single output file with gwas summary stats for all 22 chromosomes if feasible. Thanks

  • Former User of DNAx Community_96
  • 12 March 2022 00:00
  • 0 votes
  • 1 comment

• Can "Swiss Army Knife" functionality be obtained on "Cloud Workstation"?

  • Permanently deleted user
  • 11 March 2022 00:00
  • 0 votes
  • 6 comments

• When whole exome data will become available for all 450K subjects? At the moment when I create a project and dispense the data it is for 200K subjects.

  • Permanently deleted user
  • 08 March 2022 00:00
  • 0 votes
  • 1 comment

• Webinar Mar 24: Starting Cloud Analysis in the UK Biobank Research Analysis Platform

  • Brenton Pyle
  • 08 March 2022 00:00
  • 0 votes
  • 1 comment

• Where can I access to the codes used in the webinar " GWAS on Research Analysis platform using Regenie"?

  • Permanently deleted user
  • 08 March 2022 00:00
  • 0 votes
  • 1 comment

• I run vcftools for multiple files, but when I use swiss army knife and use *, I get an error as it sees my input as extra arguments, instead of running it once for each file. Is there any way to avoid merging all the vcf files into one?

  • Former User of DNAx Community_43
  • 02 March 2022 00:00
  • 0 votes
  • 1 comment

• How I can export a Jupyter lab notebook as pdf of HTML. I go to File > Export > HTML or PDF but I keep getting an error that the page is not there.

  • Permanently deleted user
  • 02 March 2022 00:00
  • 0 votes
  • 2 comments

• cram cache download/internet access from samtools

  • Permanently deleted user
  • 27 February 2022 00:00
  • 0 votes
  • 4 comments

• How to suppress job notification emails

  • Former User of DNAx Community_61
  • 25 February 2022 00:00
  • 0 votes
  • 1 comment

Featured posts

• Ongoing closure of the UKB-RAP
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• New resources for using code repositories with UK Biobank
• Useful links to DNAnexus UKB-RAP resources