• Reading data into RStudio on DNA Nexus

  • Former User of DNAx Community_63
  • 24 May 2022 00:00
  • 0 votes
  • 9 comments

• Do the multiple jobs run simultaneously by default? or does the for loop run everything sequentially?

  • Brenton Pyle
  • 23 May 2022 00:00
  • 0 votes
  • 1 comment

• We are interested in exploring the raw accelerometry data (p90001) from physical activity measurements. This data exists inside 'Bulk' folder within our project as files with '.cwa' file extension. How can we open these '.cwa' files in UK-RAP platform?

  • Former User of DNAx Community_96
  • 23 May 2022 00:00
  • 0 votes
  • 2 comments

• How to store large genotype/phenotype data on the RAP that will be queried within custom code?

  • Former User of DNAx Community_21
  • 20 May 2022 00:00
  • 0 votes
  • 1 comment

• Do you have visualizations for repeated IDPs - trajectories?

  • Brenton Pyle
  • 20 May 2022 00:00
  • 0 votes
  • 1 comment

• Making PHESANT compatible dataset from participant table

  • Former User of DNAx Community_65
  • 20 May 2022 00:00
  • 0 votes
  • 2 comments

• If you want to run commands on many large files (such as whole-genome sequencing CRAM files), won't transferring the files to project storage take a lot of time/compute?

  • Brenton Pyle
  • 19 May 2022 00:00
  • 0 votes
  • 1 comment

• JupyterLab Spark SQL queries keep hanging

  • Former User of DNAx Community_62
  • 19 May 2022 00:00
  • 0 votes
  • 3 comments

• How to install the dx toolkit. A question came up in our variant annotation workshop today about how to install the dx toolkit (the command line interface that allows you to interact with the UKBRAP). Heres documentation for that specifically:

  • Ben Busby
  • 19 May 2022 00:00
  • 0 votes
  • 3 comments

• In the Swiss Army Knife -iin parameter you can specify a whole folder, or do you need to list every single file one by one?

  • Brenton Pyle
  • 19 May 2022 00:00
  • 0 votes
  • 1 comment

• UK Biobank Project Data Update Clarification

  • Permanently deleted user
  • 17 May 2022 00:00
  • 0 votes
  • 1 comment

• Is there an updated version of plink available with the Swiss Army Knife?

  • Former User of DNAx Community_55
  • 17 May 2022 00:00
  • 0 votes
  • 2 comments

• For the chunked population wide 450k WES vcfs, where can one find a position file delimiting the start and end positions of each chunk?

  • Former User of DNAx Community_53
  • 17 May 2022 00:00
  • 0 votes
  • 9 comments

• For the WGS, where can I find a list of which samples were sequenced in each cohort (Sanger Main, Sanger Vanguard and deCODE)?

  • Permanently deleted user
  • 13 May 2022 00:00
  • 0 votes
  • 2 comments

• Why does VCFtools force the maximum allele filter to 2 on Swiss Army knife? This doesn't happen when running VCFtools outside of DNA Nexus.

  • Former User of DNAx Community_46
  • 12 May 2022 00:00
  • 0 votes
  • 4 comments

• Can you annotate with CADD, gnomad, clinvar and dbNSFP options when using hail on Spark jupyterlab notebooks?

  • Former User of DNAx Community_4
  • 06 May 2022 00:00
  • 0 votes
  • 2 comments

• Webinar June 9: Analyzing with RStudio Trial Version: Using R and RMarkdown

  • Brenton Pyle
  • 05 May 2022 00:00
  • 0 votes
  • 1 comment

• Does the EID in the main file matches with the EID in UKB RAP for the same application?

  • Former User of DNAx Community_39
  • 04 May 2022 00:00
  • 0 votes
  • 1 comment

• What is the best way to extract a list of variants from WGS data?

  • Permanently deleted user
  • 03 May 2022 00:00
  • 0 votes
  • 1 comment

• Where I can find sample codes how to LiftOver genotype data from HG37 to HG38 using Picard LiftOverVCF?

  • Permanently deleted user
  • 28 April 2022 00:00
  • 0 votes
  • 1 comment

• What is the best way to label loss-of-function variants to then perform GWAS on LoF variants and phenotypic outcome? Would a SnpEff -> SnpFilt -> Plink2 pipeline make sense? I am new to this type of research!

  • Permanently deleted user
  • 28 April 2022 00:00
  • 0 votes
  • 2 comments

• How can we download the "return" associated with a publication?

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

• Is HLA imputation available on RAP?

  • Permanently deleted user
  • 27 April 2022 00:00
  • 0 votes
  • 2 comments

• Cohort browser - Genomics - AF frequency and count not the same size as the cohort I built

  • Former User of DNAx Community_39
  • 24 April 2022 00:00
  • 0 votes
  • 2 comments

• Is there a way to view the spark UI when running jupyter notebooks?

  • Former User of DNAx Community_55
  • 22 April 2022 00:00
  • 0 votes
  • 2 comments

• Webinar May 12: Cloud Computing for HPC Users

  • Brenton Pyle
  • 22 April 2022 00:00
  • 0 votes
  • 2 comments

• What is the best way to filter each WES VCF using a list of variants of interest and merge the results?

  • Former User of DNAx Community_46
  • 22 April 2022 00:00
  • 0 votes
  • 5 comments

• Is there a way to find the record censoring dates for a particular data release version?

  • Former User of DNAx Community_57
  • 19 April 2022 00:00
  • 0 votes
  • 5 comments

• Where is dxjupyterlab-vep on spark cluster with HAIL-VEP? Cache is not found either.

  • Former User of DNAx Community_4
  • 14 April 2022 00:00
  • 0 votes
  • 4 comments

• Unable to save Hail output files

  • Former User of DNAx Community_66
  • 13 April 2022 00:00
  • 0 votes
  • 6 comments

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