• Why does dx tools still have a Python2.7 dependency? Following the directions to install does not work because of this.

  • Former User of DNAx Community_2
  • 21 July 2023 00:00
  • 0 votes
  • 1 comment

• Why is HAIL SampleQC script stalling in JupyterLab?

  • Former User of DNAx Community_82
  • 20 July 2023 00:00
  • 0 votes
  • 2 comments

• Downloading updated NMR metabolomic data

  • Former User of DNAx Community_44
  • 20 July 2023 00:00
  • 0 votes
  • 2 comments

• Taking too long to update UKB dataset

  • Former User of DNAx Community_10
  • 19 July 2023 00:00
  • 0 votes
  • 3 comments

• I am trying to generate a diet score and having hard time. Can someone help me with the analysis.

  • Former User of DNAx Community_6
  • 18 July 2023 00:00
  • 0 votes
  • 5 comments

• Dates corresponding to proteomic and metabolomic data.

  • Former User of DNAx Community_44
  • 18 July 2023 00:00
  • 0 votes
  • 3 comments

• Running HAIL-based SampleQC Script in JupyterLab

  • Former User of DNAx Community_82
  • 18 July 2023 00:00
  • 0 votes
  • 1 comment

• How to request an invoice for a bill?

  • Former User of DNAx Community_10
  • 16 July 2023 00:00
  • 0 votes
  • 3 comments

• What is the threshold value for Variant Allele Fraction and Reads on the Mutectcaller app?

  • Permanently deleted user
  • 09 July 2023 00:00
  • 0 votes
  • 3 comments

• Can I filter when convert from BAM to VCF using the Mutectcaller app?

  • Permanently deleted user
  • 09 July 2023 00:00
  • 0 votes
  • 1 comment

• How to run Genome-wide survival association analysis in DNAnexus?

  • Former User of DNAx Community_19
  • 08 July 2023 00:00
  • 0 votes
  • 1 comment

• ICD-10: L20 Atopic Dermatitis vs. Data Field 131720: Date L20 first reported

  • Former User of DNAx Community_36
  • 07 July 2023 00:00
  • 0 votes
  • 2 comments

• I am trying to figure out how to subset the protein expression dataset to participants that were randomly selected. Is there a field that denotes whether or not a participant with proteomics data is randomly selected vs preselected by the consortium?

  • Former User of DNAx Community_33
  • 07 July 2023 00:00
  • 1 vote
  • 14 comments

• Help avoiding memory issues with table exporter.

  • Former User of DNAx Community_44
  • 06 July 2023 00:00
  • 0 votes
  • 2 comments

• Can we create our custom JupyterLab image and run it on DNANexus?

  • Former User of DNAx Community_36
  • 05 July 2023 00:00
  • 0 votes
  • 1 comment

• How to best handle EID and sample name mapping for bulk WGS gVCFs?

  • Former User of DNAx Community_7
  • 03 July 2023 00:00
  • 0 votes
  • 2 comments

• How to deal with qctool Error: sample file and genotype file sample IDs do not match!

  • Former User of DNAx Community_10
  • 03 July 2023 00:00
  • 0 votes
  • 2 comments

• How do I remove intermediate files created during the WDL workflow? I can see that Terra has an option, any approach for DNAnexus? https://support.terra.bio/hc/en-us/articles/360039681632-Saving-storage-costs-by-deleting-Intermediate-files

  • Former User of DNAx Community_100
  • 01 July 2023 00:00
  • 0 votes
  • 1 comment

• Mapping ICD10 codes from field 41270 via PheWAS R package using createPhenotypes results in only ~1250 phenotypes. Does anyone know how to get ALL the phenotypes in the UKB - but particularly all related to mental disorders?

  • Former User of DNAx Community_66
  • 29 June 2023 00:00
  • 0 votes
  • 4 comments

• How to download NMR metabolomics data?

  • Former User of DNAx Community_44
  • 28 June 2023 00:00
  • 0 votes
  • 6 comments

• Will the bgenix index files be available for the WGS 200k interim, or do we have to create them?

  • Former User of DNAx Community_58
  • 27 June 2023 00:00
  • 0 votes
  • 2 comments

• Does anybody else encounter random read errors when reading imputed genotypes ?

  • Former User of DNAx Community_48
  • 26 June 2023 00:00
  • 0 votes
  • 5 comments

• How can we execute modified applets without creating duplicated data?

  • Former User of DNAx Community_55
  • 21 June 2023 00:00
  • 0 votes
  • 2 comments

• Why do our forum passwords need to be reset every 3 months?

  • Former User of DNAx Community_55
  • 21 June 2023 00:00
  • 0 votes
  • 2 comments

• Is it possible to access returned data on UKB RAP? I have identified the relevant details of the data I'm interested through the publication (return ID, etc.), though I am unable to find the data using Spark.

  • Former User of DNAx Community_33
  • 20 June 2023 00:00
  • 0 votes
  • 1 comment

• I am trying to extract a specific snip from ukb22418_cMT_b0_v2 the mitochondrial hard called chromosome file, The snps are labeled with Affx-, not rs... How do I extract a specific snp, for example Affx-34461959. The usual plink command doesn't work

  • Former User of DNAx Community_10
  • 19 June 2023 00:00
  • 0 votes
  • 2 comments

• Could you please offer the List of Field Names for All Proteins so that we can download all the proteomic data ?

  • Former User of DNAx Community_43
  • 16 June 2023 00:00
  • 0 votes
  • 2 comments

• How can I convert VCF file to tabular data?

  • Permanently deleted user
  • 14 June 2023 00:00
  • 0 votes
  • 17 comments

• I have a question about the "Haplotypes" file (the 0.06TB one - BGEN and BGI). Does this file only contained pruned SNPs after eliminating those in high LD? I am unable to understand how the haplotypes are stored here. Please Help!

  • Former User of DNAx Community_37
  • 14 June 2023 00:00
  • 0 votes
  • 3 comments

• Location for publicly available models and processed data

  • Former User of DNAx Community_64
  • 13 June 2023 00:00
  • 0 votes
  • 4 comments

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