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gatk's GenotypeGVCFs always gives an error when analyzing full exon data of.g.vcf.gz form in UK biobank: The list of input alleles must contain < NON_REF> as an allele but that is not the case at position 68991;
- Former User of DNAx Community_66
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I built a cohort including T1 structural brain images. However, the actual brain data is in the bulk folder... how can I select all the participants of my cohort in the bulk folder and download the actual data?
- Permanently deleted user
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How to use --batch-tsv with swiss army knife?
- Former User of DNAx Community_23
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How can I convert CRAM file to BAM file using Swiss Army Knife?
- Permanently deleted user
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We are trying to unzip the MRI task and rest data using jupyterLab. The project directory is read only. home/dnanexus/<my_project>; Is there a way for us to have read write access to a permanent directory. We have a student account.
- Former User of DNAx Community_74
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Where can I find the BWA Reference Genome Index file?
- Permanently deleted user
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How can I store files that aren't automatically deleted upon expiration of my Jupyter Notebook session?
- Former User of DNAx Community_97
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Is it possible to restart a single failed block within a scattered WDL task ?
- Former User of DNAx Community_48
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BOLT-LMM v2.4.1 update (added support for new bgen files)
- Permanently deleted user
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I am trying to analyze the copy number variation (CNV) files (field 22431). How can I map the entries to genes/patients?
- Permanently deleted user
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Hi- I ran the GWAS analysis using SAIGE and I had a very nosiy QQ plot and Manhattan plot. I just realized that I have not run QC steps on the imputed data. Is there a good resource on the QC steps before SAIGE analyses? Best- Nihal
- Former User of DNAx Community_91
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What's the difference between Exome sequences_Alternative exome processing and Exome sequences in the Bulk data? Is there any document where we can read about this?
- Permanently deleted user
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Can you open a port on dxjupyterlab to allow for using the dask dashboard?
- Former User of DNAx Community_38
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Using rsID to apply genomic filter on my RAP cohort
- Former User of DNAx Community_87
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There are 5 collaborators under my project, does that mean our project has 40 x 5 = 200 pounds as the initial credit? How to set up the bill for RAP activities to be charged to the 200-pound project account, not my personal 40-pound account? Thank you!
- Former User of DNAx Community_77
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SAK (bcftools) errors when streaming VCFs in batch jobs
- Permanently deleted user
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BOLT-LMM download link broken
- Former User of DNAx Community_27
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WDL: how to resume a failed workflow ? (caching)
- Former User of DNAx Community_46
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How can I capture Hail errors on the RAP?
- Former User of DNAx Community_7
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WDL: File("dx;//file-id") vs dx download
- Former User of DNAx Community_46
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Is it possible to run the FreeSurfer longitudinal processing pipeline on the RAP for T1 brain images?
- Former User of DNAx Community_49
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Potential issues with imputed data
- Former User of DNAx Community_51
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Is there a way to download phase 1 release and phase 2 release genotype calls separately? Thanks!
- Former User of DNAx Community_75
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Now I have obtained the eid numbers of patients. How can I get the exon sequencing of these specific patients?
- Former User of DNAx Community_66
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Query of the Week #1: Export Phenotypic Data to a File
- Ondrej Klempir
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Please, I am very new to the platform and still trying to understand a couple of things. How can I download demographic data and some biochemistry data for all participants from the RAP platform? the cohort browser only displays 30,000 items.
- Former User of DNAx Community_84
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