Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA.

ABSTRACT: Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration's (FDA's) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall ra

SUBMITTER: Gong B 

PROVIDER: S-EPMC11001604 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature