svim¶
SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments. It analyzes a given sorted BAM file (preferably from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.
Environment Modules¶
Run module spider svim to find out what environment modules are available for this application.
System Variables¶
- HPC_SVIMASM_DIR - installation directory
- HPC_SVIMASM_BIN - executable directory