Uncovering missed indels by leveraging unmapped reads.

ABSTRACT: In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown great accuracy in mapping short reads to the reference genome, a significant number of short reads still remain unmapped and are often excluded from downstream analyses thereby causing nonnegligible information loss in the subsequent variant calling procedure. This paper describes Genesis-indel, a computational pipeline that explores the unmapped reads to identify novel indels that are initially missed in the original procedure. Genesis-indel is applied to the unmapped reads of 30 breast cancer patients from TCGA. Results show that the unmapped reads are conserved betwee

SUBMITTER: Hasan MS 

PROVIDER: S-EPMC6668410 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature