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levioSAM2: Fast and accurate coordinate conversion between assemblies

LevioSAM2 lifts over alignments accurately and efficiently using a chain file.

Features

  • Converting SAM/BAM records from one reference to another using either a VCF file or a chain file

  • Converting alignment information, including:

    • Contig
    • Position
    • Alignmant flag
    • CIGAR string
    • Mate read information
    • MD:Z and NM:i tag (optional)

  • Multithreading support

Installation

LevioSAM2 can be installed using:

  • Conda (please make sure the version number is specified)
conda install -c conda-forge -c bioconda leviosam2

docker pull naechyun/leviosam2:latest

singularity pull docker://naechyun/leviosam2:latest
  • Built from source using CMake. See INSTALL.md for details.

Usage

LevioSAM2 performs lift-over using a chain file as the lift-over map.

Quick run:

leviosam2 index -c source_to_target.chain -p source_to_target -F target.fai
leviosam2 lift -C source_to_target.clft -a aligned_to_source.bam -p lifted_from_source -O bam

The levioSAM2 ChainMap index will be saved to source_to_target.clft. The output will be saved to lifted_from_source.bam.

See this README to learn more about running the full levioSAM2 pipeline with selective re-mapping.

Publication

Taher Mun, Nae-Chyun Chen, Ben Langmead, LevioSAM: Fast lift-over of variant-aware reference alignments, Bioinformatics, 2021;, btab396, https://doi.org/10.1093/bioinformatics/btab396