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Results of fewer SNPs total after using PJ Greer's scripts for Regenie using Plink genotype calls and final WES.
- Former User of DNAx Community_33
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how can I define a cohort without using the cohort browser?
- Former User of DNAx Community_94
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When I create a notebook in JupyterLab from the DNAnexus tab (project storage), I can't open it. Message says its a protected project. Any suggestions? Do I have too always use dx download then?
- Former User of DNAx Community_97
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Is there a map for which regions are in each 500k Whole EXOME Sequencing final release pVCF (23157) block and for the alternative gnoMAD pVCF (24068)?
- Former User of DNAx Community_94
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How to skip downloading files that already exist with dx download?
- Former User of DNAx Community_55
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Data dispensal/refresh temporarily unavailable
- Chai Fungtammasan
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Availability of pre-computed relatedness information?
- Permanently deleted user
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Assistance with LMM-BOLT through the Swiss Army Knife platform: Assertion `CompressedSNPBlocks==1' failed.
- Former User of DNAx Community_25
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How can we set a retry policy on dx run jobs?
- Former User of DNAx Community_55
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Refresh of data is been in pending since last thursday
- Former User of DNAx Community_6
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How can I estimate the recombination frequency of these 2 genes rs73182688 NLGN1 3q26.31 depression rs1501299 ADIPOQ 3q27.3 G>T BMI
- Former User of DNAx Community_10
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Selection of the GFF file version
- Former User of DNAx Community_35
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Hi, for a potential grant proposal, I want to understand how many Parkinson's patients exist in the database with the ICD-10 code Z45.1 Adjustment and management of infusion pump. Any help with this would be greatly appreciated! Thanks!
- Former User of DNAx Community_82
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Are there simpler ways of doing things?
- Former User of DNAx Community_20
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How to create an applet with the "feature" IMAGE_PROCESSING (i.e., FSL, Nipype, FreeSurfer) automatically loaded? Is this possible? I know how to load a JupyterLab instance, but was wondering if one could make an applet that automatically has these
- Former User of DNAx Community_9
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Does anyone know how to get sample ID and batch in which proteins were quantified information?
- Former User of DNAx Community_6
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Range request to only download a BAM genomic interval
- Former User of DNAx Community_46
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Running frequency counts on UKBB WGS 200K dataset leads to missing variants
- Former User of DNAx Community_80
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Hi everyone. I requested Return Data Field from UKBB, and they provided a TXT File.. They wrote that "Linkage has been undertaken such that IDs within the files correspond to IDs for your application". How do I combine that to my project? Thank you.
- Former User of DNAx Community_90
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How can I exclude with participants have specific diagnoses from my cohort using cohort browser?
- Permanently deleted user
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A mismatch in cause of death - ICD - 10 data
- Permanently deleted user
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Withdrawn participant IDs in dataset/bulk data
- Permanently deleted user
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Imputing UKB genotypes with HRC
- Former User of DNAx Community_39
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We are analyzing the WES 500K files and when I remove variants for DP, allele balance, and low complexity it seems like 15-17% (both SNPs and indels) of variants on a chromosome are being removed. Does that seem like too much?
- Former User of DNAx Community_89
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How can I extract 10 random individuals from a selected cohort in UKB RAP ?
- Former User of DNAx Community_95
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How can I exclude with participants have specific genotype from my cohort using cohort browser?
- Permanently deleted user
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How to access patient diagnoses among subset for which OLINK proteomics data exists?
- Former User of DNAx Community_6
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Issue with GEL Imputation .bgi Indicies
- Former User of DNAx Community_51
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Extract record tables using the dx command line.
- Former User of DNAx Community_60
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We highlighted a potential issue with allele frequencies for multi-allelic variants in the UKBB WGS 200k data.
- Former User of DNAx Community_58
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