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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 settings

To run the Structural Variant Caller for Long Reads tool:

        Toolbox | Long Read Support () | Structural Variant Caller for Long Reads ()

The tool accepts a single read mapping as input.

There are two calling modes, as shown in figure 9.1.

Figure 9.1: The calling mode options for Structural Variant Caller for Long Reads.

• Germline. Recommended for diploid samples. Variants with a frequency inconsistent with a diploid organism are filtered away.
• Somatic. Recommended for calling on samples where variants may appear at low frequencies. When this is enabled:
  • The diploid filtering of the Germline mode is disabled.
  • Variants are never filtered based on having too few supporting reads.
  • Strict filtering of deletions and duplications that are longer than 50,000bp is disabled.
  • Variants with frequencies between 5% and 30% are subjected to stricter filtering. This includes:
    • All variants other than long insertions are only reported if evidence for them is observed on reads mapping in both orientations.
    • Variants are filtered away if they are supported by alignments with many mismatches and indels compared to the reference.
    • Inversions and duplications are only reported if they are at least 500bp long.
    • Variants whose coverage changes by more than 10% when moving from upstream of the variant to the start position, or from the start position to the center of the variant, or from the center of the variant to the end position, or from the end position to downstream of the variant are filtered away.

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