UK Biobank Exome Sequencing Pipeline

The 302,355 UKB exome sequences were processed at AstraZeneca from their unaligned FASTQ state. A custom-built Amazon Web Services (AWS) cloud compute platform running Illumina DRAGEN Bio-IT Platform Germline Pipeline v3.0.7 was used to align the reads to the GRCh38 genome reference and perform single-nucleotide variant (SNV) and insertion and deletion (indel) calling. SNVs and indels were annotated using SnpEFF v4.3^{48 (link)} against Ensembl Build 38.92^{49 (link)}. We further annotated all variants with their genome Aggregation Database (gnomAD) MAFs (gnomAD v2.1.1 mapped to GRCh38)^{27 (link)}. We also annotated missense variants with MTR and REVEL scores^{35 (link),50 (link)}.

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Wang Q., Dhindsa R.S., Carss K., Harper A.R., Nag A., Tachmazidou I., Vitsios D., Deevi S.V., Mackay A., Muthas D., Hühn M., Monkley S., Olsson H., Wasilewski S., Smith K.R., March R., Platt A., Haefliger C, & Petrovski S. (2021). Rare variant contribution to human disease in 281,104 UK Biobank exomes. Nature, 597(7877), 527-532.

Publication 2021

DRAGEN Bio-IT Platform Germline Pipeline

Deletion Exome Genome Germline Indels Mafs Missense variants Nucleotide

Corresponding Organization : University of Melbourne

Other organizations : AstraZeneca (United States), AstraZeneca (United Kingdom), AstraZeneca (Sweden)

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Variable analysis

independent variables

Not explicitly mentioned

dependent variables

Single-nucleotide variants (SNVs)
Insertion and deletion (indel) variants

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

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