• Hi, Can you please tell me if UKBB has and shares mitochondrial DNA sequence of participants? As a researcher in a private company, am I allowed to ask for the data? And how long does it take from the data request to access to data? Thank you very much.

  • Former User of DNAx Community_81
  • 17 August 2022 00:00
  • 0 votes
  • 1 comment

• can you match plink output to EIDs?

  • Former User of DNAx Community_37
  • 16 August 2022 00:00
  • 1 vote
  • 1 comment

• How do I create a specific cohort of particular phenotypes (e.g Participants with AML)?

  • Former User of DNAx Community_2
  • 16 August 2022 00:00
  • 0 votes
  • 4 comments

• Hello, I have a question regarding launching scripts from the CLI. I submitted a batch script from the CLI. All of my scripts were completed successfully, but the output hasn't been saved. I'm not sure where I'm going wrong. Thanks for your help!

  • Former User of DNAx Community_72
  • 16 August 2022 00:00
  • 0 votes
  • 4 comments

• Hello. Do you, or anyone in the team, know if UKB now have access to all the GP records of the second half of participants in England (first half have been linked since 2016). If UKB do not have access, is there a proposed date when they will? Best wishes

  • Former User of DNAx Community_76
  • 16 August 2022 00:00
  • 0 votes
  • 3 comments

• Parallel analyses on WGS files

  • Former User of DNAx Community_56
  • 16 August 2022 00:00
  • 0 votes
  • 2 comments

• Hello, 1) are the plink files for the WGS going to be available soon? 2) I need help to run batch jobs on SAK

  • Former User of DNAx Community_56
  • 16 August 2022 00:00
  • 0 votes
  • 4 comments

• What is the best way to use git with the DNANexus platform?

  • Former User of DNAx Community_57
  • 15 August 2022 00:00
  • 0 votes
  • 4 comments

• Does the UK Biobank provides access to individual genomes/proteomes?

  • Former User of DNAx Community_50
  • 15 August 2022 00:00
  • 0 votes
  • 1 comment

• Is it possible to perform a Burden Test using a defined set of filtered variants (in a pVCF) to check for association on phenotypic expression?

  • Permanently deleted user
  • 15 August 2022 00:00
  • 0 votes
  • 1 comment

• AMA: Lora B, UK Biobank Data Analyst

  • Lora B
  • 15 August 2022 00:00
  • 0 votes
  • 8 comments

• How to easily download/mount many input files in a script or the CLI , onto the temporary worker?

  • Former User of DNAx Community_12
  • 15 August 2022 00:00
  • 0 votes
  • 1 comment

• Does anyone know why I keep getting this message on the cohort browser: 'An error occured when loading cohort count. Please try again later.'

  • Former User of DNAx Community_37
  • 14 August 2022 00:00
  • 0 votes
  • 1 comment

• Hello, I am wondering if it's possible to input a script into swissarmyknife instead of individual commands? If so, how would I do this?

  • Former User of DNAx Community_37
  • 12 August 2022 00:00
  • 0 votes
  • 1 comment

• What is the best tool to apply Hardy-Weinburg Equilibrium filtering to find variants in a pVCF with a p-value > a given threshold (10^-15)?

  • Permanently deleted user
  • 10 August 2022 00:00
  • 0 votes
  • 1 comment

• Hello, If I am looking to create a dataframe of around 200,000 participants, with individual nucleotide information regarding around 20 SNPs, what is the best way to go about doing this? Thanks :)

  • Former User of DNAx Community_37
  • 10 August 2022 00:00
  • 0 votes
  • 1 comment

• Hi folks, I have a basic question for you?how can we access the exome sequencing data (preferably as the VCFs) using HAIL on the UKB RAP?

  • Former User of DNAx Community_7
  • 10 August 2022 00:00
  • 0 votes
  • 4 comments

• Combining genotype data with phenotype data in Rstudio workbench

  • Former User of DNAx Community_40
  • 09 August 2022 00:00
  • 0 votes
  • 1 comment

• I want to liftover the genotype array calls from hg37 to hg38. I reviewed the DNAnexus liftover GitHub but I am still unsure how to perform the liftover.

  • Former User of DNAx Community_28
  • 05 August 2022 00:00
  • 0 votes
  • 3 comments

• I am performing QC as per the AD-by-proxy-GWAS guide. For this, I need to load the WES files into my JupyterNotebook but I keep getting an error.

  • Former User of DNAx Community_28
  • 04 August 2022 00:00
  • 0 votes
  • 2 comments

• How do I filter a particular exome SNP rsID for a particular EID?

  • Former User of DNAx Community_3
  • 04 August 2022 00:00
  • 0 votes
  • 6 comments

• Best way to perform Hardy-Weinberg Equilibrium filtering on WES pVCF on the RAP? Can I rely on the 'Ethnic Background' (Data-Field 21000) data field for delineation of populations?

  • Permanently deleted user
  • 02 August 2022 00:00
  • 0 votes
  • 1 comment

• What's the best way to find allele frequency for a variant in the WES data?

  • Former User of DNAx Community_28
  • 01 August 2022 00:00
  • 1 vote
  • 7 comments

• 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

Featured posts

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