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• Introduction
  • The concept of Long Read Support
  • Contact information
  • System requirements
• Template workflows
  • De Novo Assemble Long Reads and Polish with Short Reads
• Import Nanopore Reads
• De Novo Assemble Long Reads
  • De novo assembly parameters
  • De novo assembly output
• Map Long Reads to Reference
  • Map Long Reads to Reference output
• Polish with Reads
  • Polish with Reads output
• Correct Long Reads
  • Correct Long Reads output
• RNA-Seq Analysis for Long Reads
  • Reads and reference settings
  • Mapping settings
  • Expression settings
  • RNA-Seq Analysis for Long Reads output
• Structural Variant Caller for Long Reads
  • Structural Variant Caller settings
  • Structural Variant Caller output
  • Structural Variant Caller algorithm
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

Structural Variant Caller for Long Reads

The Structural Variant Caller for Long Reads tool calls structural variants of length >= 35 from long reads. The input read mapping must have been produced by the Map Long Reads to Reference tool using Long Read Support 24 or later.

The tool is designed for Whole Genome Sequencing data. Targeted sequencing is not explicitly supported. If this is necessary, a workaround may be to generate a pseudo reference genome consisting purely of the targeted regions using the Extract Annotated Regions tool (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Extract_Annotated_Regions.html).

The tool does not have specific handling for circular chromosomes. Circular chromosomes are treated as if they were linear. This means that variants near the origin may go undetected because the part of the read wrapping around the origin is ignored.

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Subsections

• Structural Variant Caller settings
• Structural Variant Caller output
• Structural Variant Caller algorithm

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