Question: What is the resolution (size of chromosomal rearrangement) that Long Ranger can detect with linked-read data?
Answer: Currently, for human data we can call and phase SNVs, indels that are less than 50 bp, and large-scale rearrangements with breakpoints that are separated by more than 30 Kb. For small SVs in the 50 bp to the 30 kb range, we can identify and phase deletions. Insertions are currently under development. You can use the --somatic flag to increase the sensitivity of large SV calls. Somatic SNV and small indel calling is not implemented in the Long Ranger pipeline.
|
Variant Class |
Germline Status |
Somatic Status |
|
SNVs |
Called & Phased |
Enabled by Data |
|
Indels (< 50bp) |
Called & Phased |
Enabled by Data |
|
Large-Scale Rearrangements (Deletions, Inversions, Translocations) > 30Kb |
Called & Phased |
Called & Phased |
|
Small SVs (Deletions, Inversions, Insertions) 50bp – 30Kb |
Deletions called & phased, Insertions under development |
Enabled by Data |