High-depth exome sequencing¶
High-depth exome sequencing specifications and data¶
Samples were run on Twist (Clinical Research Alliance) exomes and 150bp PE Novaseq 6000 sequencing (at Broad Clinical Labs). Reads were mapped to hg38 using BWA-MEM. Sequencing delivered crams with >85% bases at >20X target coverage. Full technical details are provided in the readme files with the datasets.
Data are available in vcf format, and in regenie ready-formats alongside PC and covariate files. A variety of other files are also provided.
Access for academic-only approved projects¶
Warning
The following data are only available within TRE.
44k data¶
callset:¶
This dataset is now deprecated, but is provided as it was used in the Hye In Kim, et al. Nature Genetics 2026 paper
55k data¶
crams:¶
callset:¶
(regenie results for 55k exomes are not yet released)
See also the Public data section.
For regenie step 1 use:
(for use with --bfile ; reminder to copy files to your /home/ivm first, too slow to run from standard storage)
gs://qmul-production-library-exomes-library-red/callsets/2024_05_55kCallset/release_2024-OCT-08/all_transcripts/chr1..22X_hard_filters.tidy.55273individuals.finalConsortium1_55k.alltranscriptsvep_indep-pairwise_1000_100_0.9.prune.in_extracted*
For regenie step 2 use:
(for use with --pfile ; reminder to copy files to your /home/ivm first, too slow to run from standard storage)
gs://qmul-production-library-exomes-library-red/callsets/2024_05_55kCallset/release_2024-OCT-08/all_transcripts/chr1..22X_hard_filters.tidy.55273individuals.finalConsortium1_55k.alltranscriptsvep*
Access for Consortium1 partners¶
Warning
The following data are only available within TRE.
55k data¶
crams:¶
callset:¶
Manual annotations of LoF variants (including individual level data):¶
Info
The following data are available within TRE or downloadable.
55k site-only vcf:¶
gs://qmul-production-library-consortiumpriorityperiod-green/Callsets/2024_05_55kCallset/release_2024-OCT-08/all_transcripts/
55k ExWAS Results & remeta files:¶
gs://qmul-production-library-consortiumpriorityperiod-green/Callsets/2024_05_55kCallset/release_2025-JUN-16_ExWAS/
gs://qmul-production-library-consortiumpriorityperiod-green/Callsets/2024_05_55kCallset/
Manual annotations of LoF variants:¶
Public available datasets¶
site-only vcfs and ExWAS results: see page Public data