Copy Number Variants: Methods and Protocols

1. Identification of Copy Number Variants from SNP Arrays using PennCNV

Li Fang and Kai Wang

2. Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data

Zhongyang Zhang and Ke Hao

3. Statistical Detection of Genome Differences Based on CNV Segments

Yang Zhou, Derek M. Bickhart, and George E. Liu

4. Whole Genome Shotgun Sequence CNV Detection using Read Depth

Fatma Kahveci and Can Alkan

5. Read Depth Analysis to Identify CNV in Bacteria using CNOGpro

Ola Brynildsrud

John Wiedenhoeft and Alexander Schliep

7. Split-Read InDel and Structural Variant Calling Using PINDEL

Kai Ye, Li Guo, Xiaofei Yang, Eric-Wubbo Lamijer, Keiran Raine, and Zemin Ning

8. Detecting Small Inversions using SRinversion

Ruoyan Chen, Yu Lung Lau, and Wanling Yang

9. Detection of CNVs in NGS data using VS-CNV

Nathan Fortier, Gabe Rudy, and Andreas Scherer

10. Structural Variant Breakpoint Detection with novoBreak

Zechen Chong and Ken Chen

11. Use of RAPTR-SV to Identify SVs from Read Pairing and Split Read Signatures

Derek M. Bickhart

12. Versatile Identification of Copy Number Variants with Canvas

Sergii Ivakhno and Eric Roller

13. Markov Chain Monte Carlo SV Calling with SVelter

Xuefang Zhao

Lingyang Xu, Yang Liu, Derek M. Bickhart, JunYa Li, and George E. Liu

15. Validation of Genomic Structural Variants through Long Sequencing Technologies

Xuefang Zhao

16. Structural Variation Detection and Analysis using Bionano Optical Mapping

Saki Chan, Ernest Lam, Michael Saghbini, Sven Bocklandt, Alex Hastie, Han Cao, Erik Holmlin, and Mark Borodkin