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SV inspector view

The Structural Variant (SV) inspector is a "workflow" that is designed to help users inspect structural variant calls.

We can start the SV inspector by launching it from the App level menu bar

The SV inspector can be launched from the main menu bar.
Figure: The SV inspector can be launched from the main menu bar.

This will bring up an "import form" that asks you for your SV evidence.

The following formats are supported:

  • CSV, TSV
  • VCF or VCF.gz (plain text VCF, or (b)gzipped VCF)
  • BED, BEDPE
  • STAR-fusion result file
The import form for getting started with the SV inspector.
Figure: The import form for getting started with the SV inspector.

Sources of data for SV inspector​

The SV inspector currently is designed for viewing <TRA> and breakend type entries.

Examples of variant callers that produce a VCF that can be used with the SV inspector:

Short read based:

  • Manta
  • Delly
  • Lumpy

Long read based

  • pbsv
  • Sniffles

Example SV inspector workflow​

We can start the SV inspector workflow by opening up this file containing translocation events called from a breast cancer cell line SKBR3, based on these published data.

Example VCF for use in the SV inspector​

https://jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.new.vcf

Copy this URL and paste it into the import form and select hg19:

The SV inspector with the import form and URL pasted.
Figure: The SV inspector with the import form and URL pasted.

SV inspector results​

After loading the user's requested file, you will have a tabular view with each row representing a row of the file you opened, along with a whole-genome overview of the SVs on the right

The SV inspector with loaded results.
Figure: The SV inspector with loaded results.

We can search and filter the table, with filtering and searching being reflected in the circular view as well.

The SV inspector with filter applied.
Figure: The SV inspector with filter applied.

Launching breakpoint split view​

By clicking on the features in the circular view, or clicking on the triangle drop-down on the leftmost column of the table, we can dynamically launch a new view of the data that is called the "split view" or the "breakpoint split view"

This allows us to inspect the breakpoints of the structural variant, and compare each side to the alignments.

Screenshot of the 'breakpoint split view' which examines the breakpoints of a structural variant, e.g. an interchromosomal translocation, and connects supporting reads (black splines) and the variant call itself (green thicker line, with feet indicating directionality).
Figure: Screenshot of the 'breakpoint split view' which examines the breakpoints of a structural variant, e.g. an interchromosomal translocation, and connects supporting reads (black splines) and the variant call itself (green thicker line, with feet indicating directionality).