Presented are my work as a summer research intern for 10 weeks from December 2021 to February 2022 at Kinghorn Centre for Clinical Genomics, at the Garvan Institute for Medical Research (Sydney, NSW, Australia). The outline of these works are as followed:
- Benchmarking Structural Variant Callers using Whole Genome Sequencing (WGS) Data
In our main project, we benchmarked four structural variant callers: Three from the GATK-SV workflow (Delly, Manta, Wham) and another being SvABA, against a validated true structural variant (SV) set. We are interested in the overall precision-recall performance in each caller. We used the NA12878 genome (Genome in a Bottle) as the benchmarking standard and a known, validated true SV set was assembled using previous data from Lam et al. (BMC Genomics 2016).