Related Experiment Video
Updated: Nov 4, 2025
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
LevioSAM: fast lift-over of variant-aware reference alignments
Taher Mun1, Nae-Chyun Chen1, Ben Langmead1
1Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.
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 is more than 7 times faster than an aligner when both are run with 16 threads.
Availability And Implementation:
Software Package: https://github.com/alshai/levioSAM, Experiments: https://github.com/langmead-lab/levioSAM-experiments.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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