Whole Genome Sequencing

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
- 31 October 2023 00:00
- 0 votes
- 2 comments
Efficiently extract singletons from WGS data on UKB-RAP
- Former User of DNAx Community_24
- 27 October 2023 00:00
- 0 votes
- 5 comments
Range request to only download a BAM genomic interval
- Former User of DNAx Community_46
- 06 October 2023 00:00
- 0 votes
- 1 comment
Running frequency counts on UKBB WGS 200K dataset leads to missing variants
- Former User of DNAx Community_80
- 06 October 2023 00:00
- 0 votes
- 5 comments
Snapshots bigger than instance storage
- Permanently deleted user
- 30 August 2023 00:00
- 0 votes
- 3 comments
Error when merging WGS plink files.
- Former User of DNAx Community_58
- 02 August 2023 00:00
- 0 votes
- 1 comment
How to run Genome-wide survival association analysis in DNAnexus?
- Former User of DNAx Community_19
- 08 July 2023 00:00
- 0 votes
- 1 comment
How to best handle EID and sample name mapping for bulk WGS gVCFs?
- Former User of DNAx Community_7
- 03 July 2023 00:00
- 0 votes
- 2 comments
How can I convert VCF file to tabular data?
- Permanently deleted user
- 14 June 2023 00:00
- 0 votes
- 17 comments
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
- 09 June 2023 00:00
- 0 votes
- 2 comments
Are there any annotated gds files available for ukbiobank?
- Former User of DNAx Community_6
- 29 May 2023 00:00
- 0 votes
- 2 comments
Query regarding 200k wgs dataset bgen vs Plink format files?
- Former User of DNAx Community_6
- 22 May 2023 00:00
- 0 votes
- 3 comments
Haplotype/LD analysis using TOPMed impute data
- Former User of DNAx Community_67
- 26 April 2023 00:00
- 0 votes
- 4 comments
How to use parabricks mutect2 caller on multiple .cram files?
- Former User of DNAx Community_25
- 03 April 2023 00:00
- 0 votes
- 1 comment
end_to_end_gwas_phewas/gwas-phenotype-samples-qc.ipynb
- Permanently deleted user
- 30 March 2023 00:00
- 0 votes
- 11 comments
How can I convert CRAM file to BAM file using Swiss Army Knife?
- Permanently deleted user
- 02 March 2023 00:00
- 0 votes
- 8 comments
Hi- I ran the GWAS analysis using SAIGE and I had a very nosiy QQ plot and Manhattan plot. I just realized that I have not run QC steps on the imputed data. Is there a good resource on the QC steps before SAIGE analyses? Best- Nihal
- Former User of DNAx Community_91
- 28 February 2023 00:00
- 0 votes
- 4 comments
How can I capture Hail errors on the RAP?
- Former User of DNAx Community_7
- 22 February 2023 00:00
- 0 votes
- 1 comment
Why are >2000 WGS pVCF chunks (200k release) apparently missing from the QC file 'qc_metrics_graphtyper_v2.7.1_qc.tab.gz'?
- Former User of DNAx Community_53
- 10 February 2023 00:00
- 0 votes
- 3 comments
Hi all! We were wondering if the SVs called by Graphtyper as LargeSVsize (Filter column) are considered as PASS. Thanks!
- Former User of DNAx Community_87
- 23 January 2023 00:00
- 0 votes
- 3 comments
Hi! We were wondering if it is correct to see Manta calls (23350 field_id) for 44K individuals only. Is there a date for the release of Manta call 150K? Many Thanks!
- Former User of DNAx Community_30
- 19 January 2023 00:00
- 0 votes
- 2 comments
Hi dear there Can you help me in extracting genotype data from imputed "bgen files" for certain variants using the 'bigsnpr" R package?
- Former User of DNAx Community_88
- 19 December 2022 00:00
- 0 votes
- 5 comments
Have questions about the GEL or TOPMed Impute Data Release? Ask them here!
- Chai Fungtammasan
- 19 December 2022 00:00
- 0 votes
- 22 comments
Hi all?is anyone aware of an example of code to run a PheWAS on the UKB RAP?
- Former User of DNAx Community_7
- 07 December 2022 00:00
- 0 votes
- 2 comments
Utility of Hardy-Weinberg Equilibrium filtering in UKB genomic data: p<1e-15 is not a good cutoff.
- Former User of DNAx Community_28
- 30 November 2022 00:00
- 0 votes
- 2 comments
I am analyzing the data from the 200k WGS pVCF (field 24304), and there are around 200 pVCF files per chromosome that have no variants (only the vcf file header), mostly between blocks 0 to 200. Is this intentional? Thank you!
- Former User of DNAx Community_30
- 21 November 2022 00:00
- 0 votes
- 9 comments
Expected format for 500k WGS variants?
- Former User of DNAx Community_47
- 10 November 2022 00:00
- 0 votes
- 5 comments
Is there a map for which regions are in each 200k WGS pVCF block?
- Permanently deleted user
- 09 November 2022 00:00
- 0 votes
- 10 comments
Hello, I am aware that it is not allowed to download WGS files to local machines. If I run an analysis on the RAP that takes those data as input and produces some output, will output files be downloadable? Is there any documentation on this? Andrew
- Permanently deleted user
- 09 November 2022 00:00
- 0 votes
- 3 comments
Are the PLINK files (.bed, .bim, .fam) available for use from the 200k whole genomes? At https://biobank.ndph.ox.ac.uk/showcase/field.cgi?tk=WfgiZClxpHlEjcBY9XYOIUP5JMWR5Tr9259499&id=24305, it notes that these data are "restricted"?
- Former User of DNAx Community_13
- 08 November 2022 00:00
- 0 votes
- 1 comment

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