• How do I extract certain variant from p.vcf.gz

  • Chai Fungtammasan
  • 15 December 2022 00:00
  • 0 votes
  • 1 comment

• Can someone suggest what is the best way to concatenate the .regenie files for further processing? TIA

  • Former User of DNAx Community_35
  • 13 December 2022 00:00
  • 0 votes
  • 4 comments

• dxhelper R package for decoding Phenotype Data

  • Ted Laderas
  • 13 December 2022 00:00
  • 0 votes
  • 1 comment

• How to read the UKB exome data from Python?

  • Former User of DNAx Community_97
  • 13 December 2022 00:00
  • 0 votes
  • 6 comments

• Subset WGS pVCF

  • Permanently deleted user
  • 13 December 2022 00:00
  • 0 votes
  • 1 comment

• Problems with rlang in RStudio on RAP?

  • Former User of DNAx Community_57
  • 09 December 2022 00:00
  • 0 votes
  • 2 comments

• Hi all?is anyone aware of an example of code to run a PheWAS on the UKB RAP?

  • Former User of DNAx Community_7
  • 07 December 2022 00:00
  • 0 votes
  • 2 comments

• How-to run Matlab on RAP

  • Ondrej Klempir
  • 06 December 2022 00:00
  • 0 votes
  • 4 comments

• Would it be possible to get some information for the Liver MRI? Some details about the different protocols of images available and some examples of tools that work for Liver mRI would be expressly helpful.

  • Brenton Pyle
  • 06 December 2022 00:00
  • 0 votes
  • 1 comment

• Image derived phenotype output is based on segmentation - instead of including them as a number, is it possible to provide as masks? i.e annotation of specific region to RAP/UKB returning data?

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

• DNA Nexus takes ages to run a job

  • Former User of DNAx Community_47
  • 02 December 2022 00:00
  • 0 votes
  • 2 comments

• Where is project data when using Cloud Workstation app?

  • Former User of DNAx Community_98
  • 02 December 2022 00:00
  • 0 votes
  • 1 comment

• Utility of Hardy-Weinberg Equilibrium filtering in UKB genomic data: p<1e-15 is not a good cutoff.

  • Former User of DNAx Community_28
  • 30 November 2022 00:00
  • 0 votes
  • 2 comments

• How to automatically restart jobs upon "SpotInstanceInterruption"?

  • Former User of DNAx Community_51
  • 28 November 2022 00:00
  • 1 vote
  • 3 comments

• I want to run a PheWAS analysis using PHESANT and currently trying to generate the phenotype file. I am using table exporter to extract the phenotype data for my variables of interest.

  • Former User of DNAx Community_28
  • 28 November 2022 00:00
  • 0 votes
  • 7 comments

• How to use swiss army knife with batch file?

  • Former User of DNAx Community_27
  • 24 November 2022 00:00
  • 0 votes
  • 2 comments

• Data types

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

• How to upgrade to most recent version of dx-toolkit?

  • Former User of DNAx Community_22
  • 23 November 2022 00:00
  • 0 votes
  • 5 comments

• I am analyzing the data from the 200k WGS pVCF (field 24304), and there are around 200 pVCF files per chromosome that have no variants (only the vcf file header), mostly between blocks 0 to 200. Is this intentional? Thank you!

  • Former User of DNAx Community_30
  • 21 November 2022 00:00
  • 0 votes
  • 9 comments

• Downloading or searching job logs -- where are they?

  • Former User of DNAx Community_41
  • 17 November 2022 00:00
  • 0 votes
  • 2 comments

• Hello guys: Any idea of the best way to select a cancer-free cohort to compare with cancer patients? I have tried different terms (e.g., non-cancer, cancer-free, etc.) but no good options for any of these.

  • Former User of DNAx Community_77
  • 17 November 2022 00:00
  • 0 votes
  • 2 comments

• How do you run a spark app?

  • Former User of DNAx Community_47
  • 17 November 2022 00:00
  • 0 votes
  • 7 comments

• Where can I find detailed specifications of the available instance types? I am particular interested in the GPU instances. I would like to know the GPU model, memory, etc. for each instance. Thanks!

  • Permanently deleted user
  • 11 November 2022 00:00
  • 0 votes
  • 2 comments

• What are the legal requirements for exporting a subset of the variant calls from the WGS or WES in DNAnexus to our internal (not local machine) work environment. Can we export a subset of variant calls to join with the clinical data?

  • Former User of DNAx Community_94
  • 11 November 2022 00:00
  • 0 votes
  • 1 comment

• Expected format for 500k WGS variants?

  • Former User of DNAx Community_47
  • 10 November 2022 00:00
  • 0 votes
  • 5 comments

• How can you request an increased job limit?

  • Former User of DNAx Community_47
  • 10 November 2022 00:00
  • 0 votes
  • 1 comment

• Is it possible to run a high priority app (e.g. ttyd) while many jobs are queued?

  • Former User of DNAx Community_47
  • 10 November 2022 00:00
  • 0 votes
  • 4 comments

• Is there a map for which regions are in each 200k WGS pVCF block?

  • Permanently deleted user
  • 09 November 2022 00:00
  • 0 votes
  • 10 comments

• Hello, I am aware that it is not allowed to download WGS files to local machines. If I run an analysis on the RAP that takes those data as input and produces some output, will output files be downloadable? Is there any documentation on this? Andrew

  • Permanently deleted user
  • 09 November 2022 00:00
  • 0 votes
  • 3 comments

• Trouble using $in_prefix and $in_name with swiss-army-knife

  • Former User of DNAx Community_41
  • 09 November 2022 00:00
  • 0 votes
  • 2 comments

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