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SAMtools. Bowtie: An ultrafast, memory-efficient short read aligner. LevioSAM paper and indel-aware major allele references - June 4, 2021 The levioSAM paper is out in the journal Bioinformatics LevioSAM is a tool that rapidly "lifts" alignments between reference genomes related through a VCF file.

Bowtie: An ultrafast, memory-efficient short read aligner

LevioSAM makes it easy to align to one reference with Bowtie (or other aligner), then immediately translate the alignments to a different coordinate system As a demonstration, we are adding new major-allele versions of human references (GRCh38 and h19) that contain both major-allele SNVs and major-allele (small) indels. Because they include indels, these are more comprehensive than the SNV-only major-allele reference we released previously. RNA-Seq Unified Mapper (RUM)