Skip to content

Latest commit

 

History

History
53 lines (43 loc) · 5.94 KB

dataset-prioritisation-of-sv.md

File metadata and controls

53 lines (43 loc) · 5.94 KB
Raw

Dataset visualization for article Prioritisation of Structural Variant Calls in Cancer Genomes

New Genome Browser was used to generate figures for the Prioritisation of Structural Variant Calls in Cancer Genomes article

Below are the details on how to reproduce visualization of the datasets, used in the article

Links to variations loci, provided below, will load public NGB instance located at http://ngb.opensource.epam.com

Figure 5. FGFR3-TACC3 tandem duplication fusion

  1. Navigate to FGFR3-TACC3 fusion locus (click a link to navigate to a public NGB instance)
  2. DUP (duplication) variation and read evidence will be shown
  3. Left-click a variation on a VCF track - context menu with two options will be shown
  • Show info
  • Show pair in split screen DUP
  1. Select Show pair in split screen to view second breakpoint of a duplication DUP-Splitview
  2. Left-click a variation on a VCF track again and select Show info
  3. Results of Structural Variation rearrangements will be shown (including protein domains coloring) DUP-Details

Figure 6. ROS1-SLC34A2 interchromosomal translocation fusion

  1. Navigate to ROS1-SLC34A2 fusion locus (click a link to navigate to a public NGB instance)
  2. BND (breakends) variation with alignments will be shown. Variation tooltip indicates second breakpoint location (interchromosomal translocation chr6<->chr4)
  3. Left-click a variation on a VCF track (lumpy) - context menu with two options will be shown
  • Show info
  • Show pair in split screen BND
  1. Select Show pair in split screen to view second breakpoint of a translocation Note: this location looks better when colored by Insert size, grouped by Chromosome of mate and reads view set to Collapsed To enable these modes a BAM track header menu or hotkeys could be used (default are: SHIFT+2 to set color mode, SHIFT+F to set grouping and SHIFT+X to set collapsed reads view) BND-Splitview
  2. Left-click a variation on a VCF track again and select Show info
  3. Results of Structural Variation rearrangements will be shown (including protein domains coloring) Note: there are two genes located at chr6 breakpoint, that's why two options would be shown in details window - which gene two use when renedering a visualization of rearrangement. ROS1 should be selected BND-Details

Figure 7. EML4-ALK inversion fusion

  1. Navigate to EML4-ALK fusion locus (click a link to navigate to a public NGB instance)
  2. Inversion variation with alignments will be shown
  3. Left-click a variation on a VCF track (lumpy) - context menu with two options will be shown
  • Show info
  • Show pair in split screen ALK-EML4
  1. Select Show pair in split screen to view second breakpoint of an inversion Note: this location looks better when colored by Pair orientation and sorted by Insert size . To enable these modes a BAM track header menu or hotkeys could be used (default are: SHIFT+1 to set color mode and SHIFT+Y to set sorting) ALK-EML4-Splitview
  2. Left-click a variation on a VCF track again and select Show info
  3. Results of Structural Variation rearrangements will be shown (including protein domains coloring) ALK-EML4-Details