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

Structural Variants Follow

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    Siyuan Feng

    Hi Derek,

    While I appreciate very much your definitions and illustrations of SV-related concepts, there definition for "insert size" seem to differ from other sources.

    Here, 'insert size' is defined as:

    the entire length of the DNA fragment including the adapters is called the insert size

    But it is mostly defined as the length of the DNA fragment between the adapters by many other online resources, such as Illumina and a plausible post.

    While it is fine to adopt either definition (as long as the definition is clearly made), I wonder which one applies to the Picard tool "CollectInsertSizeMetrics", as it will affect the way I interpret its output. I ask this question here because this Picard tool refer to the GATK dictionary as a reference (although not to this specific post).

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