Advanced tools and tutorials
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How can I get data from a DNA Nexus database into another format?
- Former User of DNAx Community_47
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How to submit a large input-json with dx run?
- Former User of DNAx Community_18
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ExecutorLostFailure when trying to write a matrix
- Former User of DNAx Community_22
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JupyterLab Server Connection Error
- Former User of DNAx Community_41
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OS on the computing servers?
- Permanently deleted user
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I submitted a batch of 500 jobs to UKB/RAP. The number of running jobs is always 100 and the rest in waiting. Is this defined by UKB/RAP, or is it changeable?
- Permanently deleted user
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Best alternative to lofreq in Swiss Army Knife?
- Permanently deleted user
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Is there a way to run an R script with a specified environment (snapshot) and instance type?
- Former User of DNAx Community_13
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Performing GWAS on RAP using DX toolkit and swiss-army-knife
- Former User of DNAx Community_28
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I get 'low disk space during this job' warning and my job gets aborted..im using plink via Swiss Army Knife..How can I fix this?
- Former User of DNAx Community_3
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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
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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
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dxfuse -limitedWrite on RAP?
- Permanently deleted user
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BOLT-LMM v2.4 update for RAP
- Permanently deleted user
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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
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How to run VEP docker image using swiss-army-knife?
- Former User of DNAx Community_4
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Using Tabix in Swiss-Army-Knife
- Former User of DNAx Community_88
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Multiple job failures + data retention
- Former User of DNAx Community_69
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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
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How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?
- Former User of DNAx Community_4
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If you want to run commands on many large files (such as whole-genome sequencing CRAM files), won't transferring the files to project storage take a lot of time/compute?
- Brenton Pyle
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JupyterLab Spark SQL queries keep hanging
- Former User of DNAx Community_62
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Is there an updated version of plink available with the Swiss Army Knife?
- Former User of DNAx Community_55
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Why does VCFtools force the maximum allele filter to 2 on Swiss Army knife? This doesn't happen when running VCFtools outside of DNA Nexus.
- Former User of DNAx Community_46
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Where I can find sample codes how to LiftOver genotype data from HG37 to HG38 using Picard LiftOverVCF?
- Permanently deleted user
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Is there a way to view the spark UI when running jupyter notebooks?
- Former User of DNAx Community_55
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Where is dxjupyterlab-vep on spark cluster with HAIL-VEP? Cache is not found either.
- Former User of DNAx Community_4
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Unable to save Hail output files
- Former User of DNAx Community_66
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Copying workflows within projects and copying ICD codes in cohort browser.
- Former User of DNAx Community_42
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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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