Whole Exome Sequencing
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ANNOVAR in UKB-RAP
- Lynette Sylvia Graver
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Number of sites removed by ukb23158_500k_OQFE.90pct10dp_qc_variants.txt
- Bastien Rioux
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Male heterozygotes on X chromosome
- Bastien Rioux
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Burden test from regenie in UKB WES data; the result does not contain Alleles or BETA and SE
- Former User of DNAx Community_21
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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 can I extract AD, AF, DP information from ##FORMAT lines of snpEff.vcf file?
- Permanently deleted user
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Recommendations for understanding WES pVCF file data in detail
- Former User of DNAx Community_78
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Running HAIL-based SampleQC Script in JupyterLab
- Former User of DNAx Community_82
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How to get skato to work with Regenie?
- Former User of DNAx Community_21
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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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Hello, I would like to know what would possibly be the best way of doing QC for the WES final data. Previously we have generated our in-house pipelines to QC the data in terms of genotypes and variants by using SoS in our own cluster
- Permanently deleted user
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BOLT-LMM download link broken
- Former User of DNAx Community_27
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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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How do I call the table_exporter applet from my WDL?
- Former User of DNAx Community_98
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SnpEff not labelling all LOF variants? Certain stop gained/lost or frameshift variants are not labelled as being LOF?
- Permanently deleted user
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I want to use WES data to perform analysis, but I can't find information on the exome sequencing batch. Second, are there principal components for WES data analysis?
- Former User of DNAx Community_99
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How to locate a region of interest within a chromosome while there are multiple pVCF files for that chromosome (WES data)?
- Former User of DNAx Community_23
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What is the best way to run custom python script to analyze exome data?
- Former User of DNAx Community_57
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What are your thoughts about subsetting to EA or not for WES rare variant analysis ?
- Former User of DNAx Community_95
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I am performing QC as per the AD-by-proxy-GWAS guide. For this, I need to load the WES files into my JupyterNotebook but I keep getting an error.
- Former User of DNAx Community_28
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How do I filter a particular exome SNP rsID for a particular EID?
- Former User of DNAx Community_3
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Best way to perform Hardy-Weinberg Equilibrium filtering on WES pVCF on the RAP? Can I rely on the 'Ethnic Background' (Data-Field 21000) data field for delineation of populations?
- Permanently deleted user
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What's the best way to find allele frequency for a variant in the WES data?
- Former User of DNAx Community_28
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I see that the variants in 450k_OQFE.annotations file are annotated using SNPeff, however there are no inframe deletions or insertions among the annotations. Are they filtered out, if so why? There are only LoF, synonymous and 3 categories of missense.
- Former User of DNAx Community_45
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For the chunked population wide 450k WES vcfs, where can one find a position file delimiting the start and end positions of each chunk?
- Former User of DNAx Community_53
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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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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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When whole exome data will become available for all 450K subjects? At the moment when I create a project and dispense the data it is for 200K subjects.
- Permanently deleted user
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I would like to know whether the 300k Exome data is available as a single multi-sample VCF file or are they available as multiple per chromosome, per region VCF files ? (As 977 VCFs for 200k dataset)
- Former User of DNAx Community_60
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"Are you able to suggest how long an ExWAS would take, such that I may estimate the cost?".
- Former User of DNAx Community_1
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