RT Journal Article
SR Electronic
T1 Open-source mapping and variant calling for large-scale NGS data from original base-quality scores
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.15.356360
DO 10.1101/2020.12.15.356360
A1 Krasheninina, Olga
A1 Hwang, Yih-Chii
A1 Bai, Xiaodong
A1 Zalcman, Aleksandra
A1 Maxwell, Evan
A1 Reid, Jeffrey G.
A1 Salerno, William J.
YR 2020
UL http://biorxiv.org/content/early/2020/12/16/2020.12.15.356360.abstract
AB Standardized genome informatics protocols minimize reprocessing costs and facilitate harmonization across studies if implemented in a transparent, accessible and reproducible manner. Here we define the OQFE protocol, a lossless read-mapping protocol that retains key features of existing NGS standard methods. We demonstrate that variants can be called directly from NovaSeq OQFE data without the need for base quality score recalibration and describe a large-scale variant calling protocol for OQFE data. The OQFE protocol is open-source and a containerized implementation is provided.Competing Interest StatementThe authors have declared no competing interest.