Whole Genome Sequencing

Quality control and metrics Pinned
- Lucy BG
- 20 March 2024 16:27
- 2 votes
- 1 comment
Quality control of Dragen CNV data
- Georgios Tsitsiridis
- 02 April 2026 18:27
- 0 votes
- 0 comments
How to use --batch-tsv with swiss army knife (bcftools in particular)
- Arsala Ali
- 18 February 2026 21:46
- 0 votes
- 0 comments
Analyzing VCFs of specific disease participants to see variants in a particular gene
- Arsala Ali
- 11 February 2026 17:46
- 0 votes
- 1 comment
strange WGS GWAS result with AAF>0.99 or near 0.5
- Weichen Song
- 09 February 2026 09:32
- 0 votes
- 0 comments
Request to compress and index WGS pvar files
- John J Farrell
- 05 February 2026 19:17
- 0 votes
- 0 comments
Extracting participant level SNP dosage using BCPtool query
- Bhawana Singh
- 02 February 2026 13:33
- 0 votes
- 1 comment
Covariates for ML-corrected DRAGEN pVCF
- Carmen Ramoser
- 30 January 2026 10:37
- 0 votes
- 0 comments
Filtering of UK Biobank WGS data
- Huijie Yang
- 25 January 2026 05:40
- 0 votes
- 2 comments
Swiss knife runs without error but not saving output file
- Bhawana Singh
- 22 January 2026 11:33
- 0 votes
- 5 comments
PLINK2 GWAS fails on large sample (~330k) with SpotInstanceInterruption
- Shuxin Liu
- 14 January 2026 03:36
- 0 votes
- 1 comment
ML-corrected DRAGEN pVCF genomic coordinate index file
- David Murdock
- 12 January 2026 21:49
- 0 votes
- 2 comments
High missingness in chromosome 18 DRAGEN WGS
- Thouis R Jones
- 08 January 2026 17:36
- 0 votes
- 6 comments
Error in run_ld_clumping.ipynb
- Anjin Xianyu
- 13 November 2025 01:53
- 0 votes
- 1 comment
Are sample IDs in joint-called VCF pseudonymized to match project's EIDs?
- Taiki Yamaguchi
- 04 November 2025 01:54
- 0 votes
- 2 comments
WGS BGEN files are ref-last.
- Ahmet Sayici
- 07 August 2025 09:39
- 7 votes
- 2 comments
REGENIE step2 app seems not using multi threading
- Weichen Song
- 16 July 2025 08:00
- 0 votes
- 1 comment
DRAGEN CNV and SV: is population level file avaliable?
- Weichen Song
- 05 June 2025 07:10
- 1 vote
- 3 comments
SNP filtering for genomic regions
- Ian Meneghel Danilevicz
- 29 April 2025 10:28
- 0 votes
- 3 comments
Quality Control of the DRAGEN PLINK2 WGS
- Youjie Zeng
- Edited 21 April 2025 23:09
- 0 votes
- 1 comment
faster way to analyse DRAGEN BGEN ??
- Wei-Yu Lin
- 19 April 2025 08:25
- 0 votes
- 0 comments
documentation on DRAGEN bgen and plink release
- Ruebena Ellen Dawes
- 14 April 2025 14:07
- 1 vote
- 1 comment
WGS 500k bgen format file
- Shiyu Zhang
- 11 April 2025 14:14
- 0 votes
- 0 comments
DRAGEN WGS BGEN files use 16-bit probabilities that are incompatible with Hail
- Andrew Magis
- 10 April 2025 16:30
- 1 vote
- 1 comment
WGS extracting region error
- Yevheniya Sharhorodska
- Edited 30 March 2025 20:45
- 0 votes
- 1 comment
Issue running LD Clumping: Command '['/opt/notebooks/bgen.tgz/build/apps/bgenix', '-g', 'imputed/ukb21008_c1_b0_v1.bgen', '-incl-rsids', 'rs_batch.txt']' died with <Signals.SIGABRT: 6>.
- Yiling Wang
- 18 March 2025 13:49
- 0 votes
- 0 comments
WGS quality control (read depth specifically)
- Kaitlyn Mary Price
- Edited 05 March 2025 14:34
- 0 votes
- 1 comment
Quality issues with DRAGEN joint variant callset
- Ruebena Ellen Dawes
- Edited 03 March 2025 11:08
- 3 votes
- 1 comment
500K Dragen vcf file phasing
- Yong Qian
- 23 February 2025 01:00
- 1 vote
- 1 comment
DRAGEN SV/CNV Calls
- Hayley Jane Power
- 21 February 2025 16:04
- 1 vote
- 1 comment

Didn't find what you were looking for?

New post