Performance

For details of SV² genotyping performance, please refer to the publication

---

Table of Contents

• Runtime Performance
• Genotyping Accuracy
• De novo Mutations

---

Runtime Performance

SV² runtime is dependent on coverage, the number of SVs to genotype, and the lengths of those SVs. Below is an estimate of SV² runtime, using randomly shuffled variant positions from the 1000 Genomes phase 3 release. SV² was benchmarked on one core of an Intel Xeon E5-2680v3 processor clocked to 2.5GHz, with ~20GB of RAM.

---

Genotyping Accuracy

SV² has superior genotyping accuracy when genotyping the union of SVTyper and Manta SVs. Truth sets were generated from SNV arrays and PacBio WGS. Please refer to the publication for more details.

De Novo Mutations

SV² provides stringent filters for de novo mutation discovery in the output VCF. The filters are located in the INFO column as DENOVO_FILTER=. SV² does not call variants as de novo, rather SV² DENOVO_FILTER= is a guide for filtering putative de novo mutations. For more details on how de novo filters were constructed please refer to the publication.