Structural variant calling using Sniffles2

Abstract

Structural variants (SVs) are the most common nucleotide alteration per human genome compared to other variant types and have profound implications in evolution, diseases and regulation of genes. Sniffles2 (v2.6.3) is an open-source software for reliable detection of SVs ranging from 50 bp and upward across deletions, duplications, insertions, inversions and translocations, based on long-read sequencing. The tool is commonly used for various species and has identified multiple causative mutations in human diseases, key alleles in cancer progression. Here this protocol describes how to fully use Sniffles2 to accurately identify germline and mosaic SVs. The latter are low-variant allele fraction SVs (5–22% VAF) of parts of cells. We further provide detailed instruction for SV joint calling within Sniffles2 to enable tumor/normal calling or family trio analysis, which can scale up into large-scale population studies. Sniffles2 has been benchmarked and compared to currently available tools and has the highest precision while also being very fast, able to call SVs for a 40× human genome in ~34 CPU min (~8.5 min wall clock with the default four threads). It is designed to be easy to use for researchers with basic knowledge of Linux operating systems and the terminal.