Copy number variation discovery workflows using NGS data.

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Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers.

Traditionally CNVs are identified through array based approaches but recent advances in genomic technologies, whole genome sequencing (WGS) approaches are becaming popular. Existing Next-generation sequencing (NGS)-based approaches, which detect CNVs for individual sample level, usually yield low-detection accuracy, while joint modeling approaches use maximum advantage of Mendelian transmission within the parent-offspring trio improved CNV detection accuracy. NGS data analysis pipelines for CNV discovery are available at Bitbucket | BWA MEM | CNAVnator | Pindel | SVseq2 | TrioCNV |

Figure. Distribution of the average read depth (RD) signal difference for neighboring segments on human Chr 12 (Chr12:758001-765000).