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