Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.

ABSTRACT: Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonstrated a long read length, but current interpretation methods for their novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline, PEPPER-Margin-DeepVariant, that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single-nucleotide-variant identification method at the whole-genome scale and produces high-quality single-nucleotide variants in segmental duplications

SUBMITTER: Shafin K 

PROVIDER: S-EPMC8571015 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature