Whole Genome Sequencing
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Reference genome for DRAGEN WGS 500k data?
- Robin Mjelle
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VEP annotations
- Andrew Anighoro
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Using WGS files with Hail
- Andrew Anighoro
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Microsatellite sequences quality in UKBioBiank WGS
- Marcin Wozniak
- Edited
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500K WGS Batch Information
- Yong Qian
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Question regarding batches
- Skh
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How to use Plink in RAP
- Former User of DNAx Community_28
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Hi Please, desperately I need help. I knew Data field 23370 relates to VCF files of whole genome sequencing data. I want to discover how many cases are available for malignant melanoma (WGS). I googled a lot but no clear tutorial I fund. Thanks
- Former User of DNAx Community_7
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I wonder what is the correct date of UK biobank blood sample collection that were analyzed by WGS? The platform has multiple "Date of attending..." not sure which to use to align dates from ICD codes correctly to the date of sample that was sequenced
- Former User of DNAx Community_23
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Is there a way to download WGS data? Could it be preprocessed on RAP then downloaded if direct download isn't possible?
- Former User of DNAx Community_6
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Are 500K WGS (GATK) and 200K WGS cram files the same for the same sample ids even though they have different fieldids? How much differences do we expect from the GATK crams and Dragen crams in the 500K WGS? Should we use DRAGEN cram?
- Permanently deleted user
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New Data release on UKB-RAP: WGS Data from 500,000 Participants, Proteomics Data & Updated Imaging Data
- Brenton Pyle
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How can I find the common variants in my VCF files?
- Permanently deleted user
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How should I get allele frequencies for a specific cohort as per the WGS on the UKB RAP?
- Former User of DNAx Community_29
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Anyone know of a good workflow/tools to look at trisonomy in the 500K cohort? I don't have much experience with CNVs so beginner level explanations would be much appreciated, thanks!
- Former User of DNAx Community_16
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Efficiently extract singletons from WGS data on UKB-RAP
- Former User of DNAx Community_24
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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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Snapshots bigger than instance storage
- Permanently deleted user
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Error when merging WGS plink files.
- Former User of DNAx Community_58
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How to run Genome-wide survival association analysis in DNAnexus?
- Former User of DNAx Community_19
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How to best handle EID and sample name mapping for bulk WGS gVCFs?
- Former User of DNAx Community_7
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How can I convert VCF file to tabular data?
- Permanently deleted user
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Hi everyone, I am running Regenie form the RAP Command line. I got tis error "set file : [ukb23158_500k_OQFE.sets.txt.gz] ERROR: unknown chromosome code in set list file". I am using the files already available on UKBiobank RAP.
- Former User of DNAx Community_89
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Are there any annotated gds files available for ukbiobank?
- Former User of DNAx Community_6
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Query regarding 200k wgs dataset bgen vs Plink format files?
- Former User of DNAx Community_6
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Haplotype/LD analysis using TOPMed impute data
- Former User of DNAx Community_67
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How to use parabricks mutect2 caller on multiple .cram files?
- Former User of DNAx Community_25
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end_to_end_gwas_phewas/gwas-phenotype-samples-qc.ipynb
- Permanently deleted user
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How can I convert CRAM file to BAM file using Swiss Army Knife?
- Permanently deleted user
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