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. 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.
Along with the paper and software, we are also releasing tutorial instructions on how to use levioSAM in common scenarios. One key scenario is where the user would like to align reads to a major-allele reference, then immediately translate the alignments back to the typical reference. To enable this, we released new major-allele reference indexes for Bowtie and Bowtie 2 (see right-hand sidebar) that include major-allele indels and corresponding levioSAM indexes. It’s now easily than ever to align to a high-quality indel-aware major-allele reference, but get alignments to the typical reference at the end of the day!