Whole Genome Sequencing

Quality control and metrics Pinned
- Lucy BG
- 20 March 2024 16:27
- 2 votes
- 0 comments
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
- 0 comments
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
- 0 votes
- 0 comments
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
- 0 comments
Quality issues with DRAGEN joint variant callset
- Ruebena Ellen Dawes
- Edited 03 March 2025 11:08
- 2 votes
- 0 comments
500K Dragen vcf file phasing
- Yong Qian
- 23 February 2025 01:00
- 0 votes
- 0 comments
DRAGEN SV/CNV Calls
- Hayley Jane Power
- 21 February 2025 16:04
- 1 vote
- 0 comments
Cost effective use of python tool
- Liam McIntyre
- 02 January 2025 04:28
- 0 votes
- 0 comments
Optimising speed of extracting specific loci from WGS
- Gabriel Doctor
- Edited 26 November 2024 10:46
- 0 votes
- 0 comments
Issues Accessing .bgen Files and Role of .bgi Files in LD Clumping
- Alexander Yaacov Peres
- 19 November 2024 20:37
- 0 votes
- 2 comments
Can I continue a job which failed before because billing account reached its spending limit?
- Yiming Qin
- 19 October 2024 08:38
- 0 votes
- 3 comments
SAIGE GWAS - Single variant association tests cannot work
- Shangyou Zheng
- 08 October 2024 11:42
- 0 votes
- 1 comment
participant IDs in individual VCFs
- Tammy Lau
- 05 August 2024 18:37
- 0 votes
- 2 comments
Missing homozygous variant calls in querying Dragen WGS gvcf files
- Srikanth Jammulapati
- 31 July 2024 17:06
- 0 votes
- 0 comments
How to combine multiple vcfs as single using dnanexus
- Akhil Pampana
- 31 July 2024 15:47
- 0 votes
- 3 comments
Extracting group of samples from 500K WGS pvcf files
- Jonny James Else
- 30 July 2024 09:08
- 0 votes
- 4 comments
FOR HELP- RUN LD Clumping
- Rufu Chen
- 09 June 2024 16:07
- 0 votes
- 8 comments
WGS 500k PLINK and BGEN
- Andrew Haddad
- 27 May 2024 14:52
- 0 votes
- 4 comments
500K WGS batch IDs and GRCh38 coordinates
- Sourena Soheili-Nezhad
- 06 May 2024 13:15
- 1 vote
- 5 comments
How to match EIDs with rsIDs?
- Fariba Ahmadizar
- 18 April 2024 05:48
- 0 votes
- 2 comments
Unable to view cram files with pysam due to truncation error?
- Sohaib Rumi Ansari
- 28 March 2024 12:18
- 0 votes
- 0 comments
Which RAP tools work natively with the segmentation of the genome into tiny chunks (with no index)
- James Eales
- 26 March 2024 00:23
- 3 votes
- 12 comments
GWAS Analysis Using pVCF Format Data
- Yingzhou Shi
- Edited 23 March 2024 16:33
- 0 votes
- 3 comments
Reference genome for DRAGEN WGS 500k data?
- Robin Mjelle
- 15 March 2024 09:23
- 0 votes
- 5 comments
VEP annotations
- Andrew Anighoro
- 29 February 2024 16:25
- 1 vote
- 2 comments
Using WGS files with Hail
- Andrew Anighoro
- 29 February 2024 16:02
- 0 votes
- 7 comments

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