Insights from a genome-wide truth set of tandem repeat variation.

ABSTRACT: Tools for genotyping tandem repeats (TRs) from short read sequencing data have improved significantly over the past decade. Extensive comparisons of these tools to gold standard diagnostic methods like RP-PCR have confirmed their accuracy for tens to hundreds of well-studied loci. However, a scarcity of high-quality orthogonal truth data limited our ability to measure tool accuracy for the millions of other loci throughout the genome. To address this, we developed a TR truth set based on the Synthetic Diploid Benchmark (SynDip). By identifying the subset of insertions and deletions that represent TR expansions or contractions with motifs between 2 and 50 base pairs, we obtained accurate genotypes for 139,795 pure and 6,845 interrupted repeats in a single diploid sample. Our approach did no

SUBMITTER: Weisburd B 

PROVIDER: S-EPMC10197592 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature