Whole Genome Sequencing

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
How to use R-based PLINK plug-in in RAP?
- Former User of DNAx Community_26
- 07 November 2022 00:00
- 0 votes
- 5 comments
Best approach annotating variants with CADD and gnomAD
- Former User of DNAx Community_29
- 19 October 2022 00:00
- 0 votes
- 3 comments
SNP IDs in WGS
- Former User of DNAx Community_56
- 12 October 2022 00:00
- 0 votes
- 4 comments
I am trying to find WGS vcf files. I see individual-level vcf files per sample. Where can I find joined called vcf files for WGS located? Please do let me know how to access those and use them for the extraction of the gene region I am interested in.?
- Former User of DNAx Community_6
- 12 October 2022 00:00
- 0 votes
- 8 comments
Will there be UKB WGS PLINK bfiles?
- Former User of DNAx Community_4
- 06 October 2022 00:00
- 1 vote
- 4 comments
Extract multiple regions from CRAM with samtools view on the RAP
- Permanently deleted user
- 04 October 2022 00:00
- 0 votes
- 15 comments
Are UKB pVCF wes files truly bgzipped?
- Former User of DNAx Community_22
- 03 October 2022 00:00
- 0 votes
- 2 comments
The sample code to load a VCF file with Hail is failing for me when I try it on a single 6 Gb VCF from the whole genome pVCFs. Can you help me to resolve this error?
- Former User of DNAx Community_47
- 30 September 2022 00:00
- 0 votes
- 3 comments
Hello, When looking at a specific variant in a cohort in the Genomics tab, is it possible have access to IDs of the patients having this specific variant ? Thank you !
- Former User of DNAx Community_74
- 20 September 2022 00:00
- 0 votes
- 4 comments
WGS cram files truncated?
- Permanently deleted user
- 19 September 2022 00:00
- 0 votes
- 3 comments
How to fix QCtool code to filter bgen file?
- Former User of DNAx Community_40
- 07 September 2022 00:00
- 0 votes
- 8 comments
dx error: unrecognized arguments for REGENIE
- Former User of DNAx Community_52
- 06 September 2022 00:00
- 0 votes
- 5 comments
Issue retrieving the data field 23196 ? Whole genome GATK joint call pVCF
- Former User of DNAx Community_30
- 06 September 2022 00:00
- 0 votes
- 1 comment
Whole genome GraphTyper joint call pVCF README with chromosome section specification
- Former User of DNAx Community_30
- 06 September 2022 00:00
- 0 votes
- 1 comment
Best resources for joint call pVCF exploration?
- Former User of DNAx Community_30
- 06 September 2022 00:00
- 0 votes
- 3 comments
Get EID of variant carriers from pVCF?
- Permanently deleted user
- 23 August 2022 00:00
- 0 votes
- 5 comments

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