Whole Genome Sequencing
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Quality control and metrics Pinned
- Lucy BG
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Optimising speed of extracting specific loci from WGS
- Gabriel Doctor
- Edited
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Issues Accessing .bgen Files and Role of .bgi Files in LD Clumping
- Alexander Yaacov Peres
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Can I continue a job which failed before because billing account reached its spending limit?
- Yiming Qin
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SAIGE GWAS - Single variant association tests cannot work
- Shangyou Zheng
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participant IDs in individual VCFs
- Tammy Lau
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Missing homozygous variant calls in querying Dragen WGS gvcf files
- Srikanth Jammulapati
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How to combine multiple vcfs as single using dnanexus
- Akhil Pampana
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Extracting group of samples from 500K WGS pvcf files
- Jonny James Else
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FOR HELP- RUN LD Clumping
- Rufu Chen
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WGS 500k PLINK and BGEN
- Andrew Haddad
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500K WGS batch IDs and GRCh38 coordinates
- Sourena Soheili-Nezhad
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How to match EIDs with rsIDs?
- Fariba Ahmadizar
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Unable to view cram files with pysam due to truncation error?
- Sohaib Rumi Ansari
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Which RAP tools work natively with the segmentation of the genome into tiny chunks (with no index)
- James Eales
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GWAS Analysis Using pVCF Format Data
- Yingzhou Shi
- Edited
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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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