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bioRxiv · 10.1101/2021.02.05.429867

LevioSAM: Fast lift-over of alternate reference alignments

Mun, T.·Chen, N.-C.·Langmead, B.
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Abstract

MotivationAs 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. ResultsLevioSAM 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. Availabilityhttps://github.com/alshai/levioSAM Contacttmun1@jhu.edu, langmea@cs.jhu.edu

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Mun, T., Chen, N.-C., Langmead, B.. 2021-02-05. LevioSAM: Fast lift-over of alternate reference alignments. https://doi.org/10.1101/2021.02.05.429867

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