Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

StructuralVariationDiscoveryPipelineSpark vs GermlineCNVCaller


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    Pamela Bretscher

    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,


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