RT Journal Article
SR Electronic
T1 LevioSAM: Fast lift-over of alternate reference alignments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.02.05.429867
DO 10.1101/2021.02.05.429867
A1 Taher Mun
A1 Nae-Chyun Chen
A1 Ben Langmead
YR 2021
UL http://biorxiv.org/content/early/2021/02/05/2021.02.05.429867.abstract
AB Motivation As more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.Results LevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads.Availability https://github.com/alshai/levioSAMContact tmun1{at}jhu.edu, langmea{at}cs.jhu.eduCompeting Interest StatementThe authors have declared no competing interest.