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For the WGS, where can I find a list of which samples were sequenced in each cohort (Sanger Main, Sanger Vanguard and deCODE)?
- Permanently deleted user
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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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Can you annotate with CADD, gnomad, clinvar and dbNSFP options when using hail on Spark jupyterlab notebooks?
- Former User of DNAx Community_4
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Does the EID in the main file matches with the EID in UKB RAP for the same application?
- Former User of DNAx Community_39
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What is the best way to extract a list of variants from WGS data?
- Permanently deleted user
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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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What is the best way to label loss-of-function variants to then perform GWAS on LoF variants and phenotypic outcome? Would a SnpEff -> SnpFilt -> Plink2 pipeline make sense? I am new to this type of research!
- Permanently deleted user
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How can we download the "return" associated with a publication?
- Permanently deleted user
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Is HLA imputation available on RAP?
- Permanently deleted user
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Cohort browser - Genomics - AF frequency and count not the same size as the cohort I built
- Former User of DNAx Community_39
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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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Webinar May 12: Cloud Computing for HPC Users
- Brenton Pyle
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What is the best way to filter each WES VCF using a list of variants of interest and merge the results?
- Former User of DNAx Community_46
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Is there a way to find the record censoring dates for a particular data release version?
- Former User of DNAx Community_57
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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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April Ask Me Anything: Imaging Analysis
- Brenton Pyle
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I want to locate the pVCF UKB23352_c19 file that has position chr19:17642033-17642056. There are 1000 files. How do I do it?
- Former User of DNAx Community_10
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Hi, I am new to DNAnexus. I want to create a project. However, I met an error which is "The application is not enabled for RAP". I do have a UKB project and I enter the specific application ID. I wonder if you can help me? Thank you~
- Former User of DNAx Community_83
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Is it expected that some WGS GraphTyper pVCF files have no variants?
- Permanently deleted user
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How can I identify which subjects have which alleles of rs56041637 in the WGS data? rs56041637 is an intron variant not in the imputed snps. https://www.ncbi.nlm.nih.gov/snp/rs56041637
- Former User of DNAx Community_10
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Why 0 participants but 416.36TiB of data?
- Former User of DNAx Community_39
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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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I am a student researcher who is unsure about the financial impact of UKB RAP. Has anyone in a similar situation had any experience applying for enhanced credits and could share if it is easy to apply, and how to gauge if I'm likely to run out of credit?
- Former User of DNAx Community_31
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How do I load .p.vcf.gz files into the python environment on the spark cluster? Do I need to use dxdata?
- Former User of DNAx Community_4
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Hi, By whom and how were the helper filer for the 450K exomes generated? Has any filtering been applied for the pVCF or the plink files? Is the release on the RAP from this pipeline? https://www.nature.com/articles/s41586-021-04103-z
- Former User of DNAx Community_79
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Is it possible to define a cohort using Cohort Browser that has a set of inpatient ICD9/ICD10 OR death ICD9/ICD10 codes? So far I am only able to define a cohort with a set of inpatient ICD9/ICD10 codes WITH death ICD9/ICD10 codes.
- Former User of DNAx Community_46
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