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SV inspector view

The SV inspector is a combined variant table and whole-genome circular view for triaging structural variant calls.

For an end-to-end walkthrough using real cancer sequencing data, see the C-GIAB tutorial.

Launch it from the main menu bar:

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

An import form will appear asking for your SV data.

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.
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.

Compatible variant callers:

Short read based:

  • Manta
  • Delly
  • Lumpy

Long read based

  • pbsv
  • Sniffles

Example SV inspector workflow​

As an example, load this file of translocation events called from the SKBR3 breast cancer cell line (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.
The SV inspector with the import form and URL pasted.

SV inspector results​

The loaded file appears as a searchable table with each row representing one variant, alongside a whole-genome circular overview.

The SV inspector with loaded results.
The SV inspector with loaded results.

Table filters are reflected in the circular view.

The SV inspector with filter applied.
The SV inspector with filter applied.

Launching breakpoint split view​

Click a feature in the circular view, or the triangle dropdown on any table row, to open the breakpoint split view for that variant.

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).
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).