LevioSAM: Fast lift-over of alternate reference alignments
biorxiv(2021)
摘要
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
Contact tmun1{at}jhu.edu, langmea{at}cs.jhu.edu
### Competing Interest Statement
The authors have declared no competing interest.
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