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22 papers · 1 filter
Finding easy regions for short-read variant calling from pangenome data
Heng Li
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without s…
BWT construction and search at the terabase scale
Heng Li
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant…
Interpreting artificial neural networks to detect genome-wide association signals for complex traits
Burak Yelmen, Maris Alver, Merve Nur Güler +3
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although geno…
Exploring gene content with pangene graphs
Heng Li, Maximillian Marin, Maha Reda Farhat
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to iden…
Beyond the exome: what's next in diagnostic testing for Mendelian conditions
Monica H. Wojcik, Chloe M. Reuter, Shruti Marwaha +21
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise…
Variant interpretation using population databases: lessons from gnomAD
Sanna Gudmundsson, Moriel Singer-Berk, Nicholas A. Watts +7
Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variati…