domains / families / science / longread-sv-pipeline

longread-sv-pipeline

separate

Orchestrates an end-to-end long-read structural-variant pipeline - basecalling to minimap2 alignment (platform-matched preset) to Sniffles2/cuteSV/pbsv calling to optional assembly-based calling (dipcall/PAV) to two-step .snf cohort merging to Truvari benchmarking - chaining ONT and PacBio HiFi runs while handing the SV signal mechanism off to the component skills. Use when running a long-read SV workflow from reads to a benchmarked callset, choosing the minimap2 preset and SV caller by platform and goal, deciding when long reads are worth it for the insertions and repeat-mediated SVs short reads physically miss, building a joint-genotyped cohort with the two-step .snf design, or parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG. Not for the SV signal mechanism itself (see variant-calling/structural-variant-calling) or short-read SV.

When to use

• running a long-read SV workflow from reads to a benchmarked callset
• choosing the minimap2 preset and SV caller by platform and goal
• deciding when long reads are worth it for insertions and repeat-mediated SVs
• building a joint-genotyped cohort with the two-step .snf design
• parameterizing a Truvari benchmark against GIAB HG002 Tier 1 plus CMRG

When not to use

• the SV signal mechanism itself
• short-read SV

Skill page

Source