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What cost an almost finish job shifts to wait status and restart?
- Permanently deleted user
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How to use Ensembl Variant Effect Predictor(VEP) on UKB data for GWAS?
- Former User of DNAx Community_24
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Can I use GLnexus to create a pVCF for all of the females (273k people) in the UKB cohort?
- Former User of DNAx Community_32
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Attempt to retrieve all data fields from a cohort failed in dxjupyter notebook. I am wondering what the error means and the best practice for retrieving all fields for every participant may be.
- Former User of DNAx Community_26
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How to define a cohort from a list of EIDs?
- Former User of DNAx Community_26
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Dear DNAnexsus team, Is it possible to turn the cohort browsers filters once a cohort has been generated into "code" for reproducibility/ more CLI orientated members of our team? Many thanks
- Former User of DNAx Community_45
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Dementia Researcher Roundtable Mar 31: Working with Large-Scale Datasets to Enable Discovery
- Brenton Pyle
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How can I run regenie step 2 for all 22 chromosomes at once? I would like regenie to spit out a single output file with gwas summary stats for all 22 chromosomes if feasible. Thanks
- Former User of DNAx Community_96
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Can "Swiss Army Knife" functionality be obtained on "Cloud Workstation"?
- Permanently deleted user
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When whole exome data will become available for all 450K subjects? At the moment when I create a project and dispense the data it is for 200K subjects.
- Permanently deleted user
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Where can I access to the codes used in the webinar " GWAS on Research Analysis platform using Regenie"?
- Permanently deleted user
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I run vcftools for multiple files, but when I use swiss army knife and use *, I get an error as it sees my input as extra arguments, instead of running it once for each file. Is there any way to avoid merging all the vcf files into one?
- Former User of DNAx Community_43
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How I can export a Jupyter lab notebook as pdf of HTML. I go to File > Export > HTML or PDF but I keep getting an error that the page is not there.
- Permanently deleted user
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cram cache download/internet access from samtools
- Permanently deleted user
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How to suppress job notification emails
- Former User of DNAx Community_61
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Are there alignment reports available?
- Permanently deleted user
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Are the unplaced contigs of Hg38 included in the alignments?
- Permanently deleted user
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Is there a way to mount Project/Bucket folders on VM workers directly, like NFS mount?
- Permanently deleted user
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Failed to visualize data
- Former User of DNAx Community_61
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Just wondering if there is dx commands that is equivalent to: find /path -name "*.bam" that can list all bam files with complete paths under /path directory. If not how about something like ls */*/*.bam? Thanks for help.
- Permanently deleted user
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DXSearchERror encountered when running OpenBio notebook
- Former User of DNAx Community_7
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Webinar Feb 24: Visualizing and Annotating GWAS Results on the UK Biobank Research Analysis Platform
- Brenton Pyle
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Subsetting by genome
- Former User of DNAx Community_45
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Hi, can you give me an idea how to proceed with this; I have an existing series of perl scripts (a few thousand lines), to perform variant calling from cram files. Is there anyway I can translate my current approach onto the Dnanexus system? Thanks
- Former User of DNAx Community_80
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Hi! Question: How to retrieve all fields (from phenotypic data) for a specific sample or list of samples (provided a file for example)?
- Former User of DNAx Community_85
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Hi folks! Ask me anything about UKBRAP or bioinformatics in general! Starting in 90 minutes!
- Ben Busby
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I am trying to set up ssh settings so I can run a workstation. I am getting the following error when trying to run the command using CLI on a windows workstation. I have installed python version 3 and reinstalled dx CLI. Many thanks for your help!
- Former User of DNAx Community_45
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