T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population.

ABSTRACT: The T2T-CHM13 reference genome, released in March 2022, fills in the 8% of the human genome that was not resolved in GRCh38 and reconstructs large parts of the known genome. The more accurate and complete reference genome is expected to improve the quality of read mapping and variant calling. Even though whole-genome sequencing (WGS)-based approaches have become the gold standard in medical genetics, the extent of the benefits of the improved reference genome remains unclear. In this study, we aim to evaluate alignment and variant call performance with T2T-CHM13 as a reference using a cross-sectional Swedish cohort (SweGen) comprising 1000 individuals with short-read Illumina WGS data available. Remapping and variant calling is performed using the nf-core/sarek pipeline. T2T-CHM13 improves

SUBMITTER: Schmitz D 

PROVIDER: S-EPMC12581843 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature