• When I generate a new file in a JupyterLab notebook and upload it to my project storage, I cannot access that file in the same session, even if I refresh. I get the error that the file does not exist.

  • Former User of DNAx Community_13
  • 29 July 2022 00:00
  • 0 votes
  • 1 comment

• For pVCF best practices how do I reference the GRCh38 fasta? The documentation provides: bcftools norm -m - -f <reference> -Oz -o <normVCF> <inputVCF> as the call to use but I do not know how to designate path to grc38.reference.fasta

  • Permanently deleted user
  • 28 July 2022 00:00
  • 0 votes
  • 4 comments

• How to merge VCF files with Swiss Army Knife?

  • Former User of DNAx Community_56
  • 28 July 2022 00:00
  • 0 votes
  • 8 comments

• I'm having difficulty install the R package devtools, has anyone else had success installing this package?

  • Former User of DNAx Community_13
  • 27 July 2022 00:00
  • 0 votes
  • 6 comments

• Webinar Aug 25: UK Biobank Research Analysis Platform Overview

  • Brenton Pyle
  • 26 July 2022 00:00
  • 0 votes
  • 1 comment

• dxfuse -limitedWrite on RAP?

  • Permanently deleted user
  • 23 July 2022 00:00
  • 0 votes
  • 2 comments

• BOLT-LMM v2.4 update for RAP

  • Permanently deleted user
  • 23 July 2022 00:00
  • 0 votes
  • 4 comments

• Best practices for backups on RAP?

  • Permanently deleted user
  • 23 July 2022 00:00
  • 0 votes
  • 5 comments

• Best way to run the same command on all CRAM files?

  • Permanently deleted user
  • 19 July 2022 00:00
  • 0 votes
  • 3 comments

• How to use dxFUSE style file paths in Swiss Army Knife?

  • Permanently deleted user
  • 18 July 2022 00:00
  • 0 votes
  • 2 comments

• Are WES pVCF files (Data-Field 23148) already filtered for Genotype depth (SNV DP >= 7, INDEL DP>=10) and allele balance filters (hetzyg SNV AB >0.15, hetzyg INDEL<0.2)?

  • Permanently deleted user
  • 17 July 2022 00:00
  • 0 votes
  • 4 comments

• In a workflow, how to not upload intermediate files and only upload the output of the final step?

  • Former User of DNAx Community_12
  • 14 July 2022 00:00
  • 0 votes
  • 2 comments

• Does anyone have a good tutorial on Eigensoft for use in DNAnexus?

  • Former User of DNAx Community_33
  • 13 July 2022 00:00
  • 0 votes
  • 5 comments

• UK Biobank Cohort Update with Dataset Refresh

  • Permanently deleted user
  • 12 July 2022 00:00
  • 0 votes
  • 2 comments

• How to run VEP docker image using swiss-army-knife?

  • Former User of DNAx Community_4
  • 08 July 2022 00:00
  • 0 votes
  • 4 comments

• Best way to view a full VCF file?

  • Permanently deleted user
  • 05 July 2022 00:00
  • 0 votes
  • 1 comment

• Using Tabix in Swiss-Army-Knife

  • Former User of DNAx Community_88
  • 30 June 2022 00:00
  • 0 votes
  • 2 comments

• Webinar Sept 27: Analysis of Accelerometer and Metabolomic Data in the UK Biobank Dataset

  • Brenton Pyle
  • 22 June 2022 00:00
  • 0 votes
  • 6 comments

• Is it possible to run Regenie step 2 with whole genome data rather than whole exome data considering that it is in pVCF format and there are more than 1 file for each chromosome?

  • Permanently deleted user
  • 14 June 2022 00:00
  • 0 votes
  • 1 comment

• Is there a way to designate exclusions of participants whose genetic sex (DF: 22001) does not match their reported sex (DF: 31) within the cohort browser?

  • Permanently deleted user
  • 13 June 2022 00:00
  • 0 votes
  • 3 comments

• Not able to view data for all chromosomes on IGV

  • Former User of DNAx Community_73
  • 13 June 2022 00:00
  • 0 votes
  • 2 comments

• Multiple job failures + data retention

  • Former User of DNAx Community_69
  • 10 June 2022 00:00
  • 0 votes
  • 4 comments

• Webinar July 14: Analyzing the UK Biobank Dataset with RStudio Workbench

  • Brenton Pyle
  • 10 June 2022 00:00
  • 0 votes
  • 1 comment

• Best strategy for annotating and filtering VCF files using VEP on UKB RAP?

  • Former User of DNAx Community_4
  • 10 June 2022 00:00
  • 0 votes
  • 1 comment

• Have questions about the 200k WGS Joint Variant Call Data Release? Ask them here!

  • Brenton Pyle
  • 08 June 2022 00:00
  • 0 votes
  • 24 comments

• I see that the variants in 450k_OQFE.annotations file are annotated using SNPeff, however there are no inframe deletions or insertions among the annotations. Are they filtered out, if so why? There are only LoF, synonymous and 3 categories of missense.

  • Former User of DNAx Community_45
  • 07 June 2022 00:00
  • 0 votes
  • 1 comment

• New 200k WGS Joint Variant Call Data Release

  • Brenton Pyle
  • 07 June 2022 00:00
  • 0 votes
  • 1 comment

• If I do not see the BIM, MAP, FAM files on my approved database, does this mean that I do not have access to genotype results of chromosomes 1-22?

  • Former User of DNAx Community_91
  • 05 June 2022 00:00
  • 0 votes
  • 2 comments

• It seems that the recently dx uploaded files does not show up on /mnt/project until I re-start the whole Jupyter Lab VM

  • Brenton Pyle
  • 02 June 2022 00:00
  • 0 votes
  • 7 comments

• What about something as simple as retrieving the file names (i.e., as would be done with ls or find). Do these also need to be sent through a dx run request? What about visualizing the output (i.e., cat, less..)?

  • Brenton Pyle
  • 01 June 2022 00:00
  • 0 votes
  • 1 comment

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