StructuralVariationDiscoveryPipelineSpark vs GermlineCNVCaller

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Heba B abusamra

• November 15, 2021 08:26

Dear 

I need to understand the difference between StructuralVariationDiscoveryPipelineSpark tool and  GermlineCNVCaller

As I knowledge the CNV is part of SV  "Structural variation (SV) is generally defined as a region of DNA approximately 1 kb and larger in size and can include inversions and balanced translocations or genomic imbalances (insertions and deletions), commonly referred to as copy number variants (CNVs)."

What SV detection method is used by StructuralVariationDiscoveryPipeline? read depth, read-pair, split read, or assembly?

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  Pamela Bretscher

  • November 15, 2021 15:36

  Hi Heba B abusamra,

  You are correct that Copy Number Variants (CNVs) are one specific type of structural variant. Structural variants also include translocations and inversions which are not CNVs. You can read about the algorithms and methods for structural variation discovery in the tool documentation. The StructuralVariationDiscoveryPipelineSpark tool utilizes the algorithms from FindBreakpointEvidenceSpark which combines evidence from split reads, discordant read pairs, template-length anomalies, and copy number variation. I hope this is helpful and please let me know if you have any additional questions. 

  Kind regards,

  Pamela

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