• 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

• What is the typical time taken to launch a JupyterLab instance? My regular instance (not Spark) has been in "Launching" state for the last 16 minutes. This seems like an excessive amount of time taken to launch. How long does this typically take?

  • Former User of DNAx Community_70
  • 01 June 2022 00:00
  • 1 vote
  • 2 comments

• Will OCT Converter be implemented in the future? i.e the OCT iamges are *.FDS and *.FDA files

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

• Questions about data in gp_scripts table from UKB

  • Former User of DNAx Community_62
  • 26 May 2022 00:00
  • 0 votes
  • 2 comments

• How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?

  • Former User of DNAx Community_4
  • 26 May 2022 00:00
  • 0 votes
  • 1 comment

• Is ?project? the literal name of this particular project, or it would be ?project? regardless of the actual project name?

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

• Is it useful to convert .nii.gz files to .nii - and what is the difference between the two formats?

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

• Would someone with RAP experience working on annotating VCF files for loss-of-function variants be willing to connect and offer tips/advice? I am new to the field and am feeling rather overwhelmed!

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

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