User Interface

When reviewing variants you’ll have the following view:

_images/overview.png

There are two main sections in this view: the Snoopy interface and the Dalliance interface.

_images/overview_split.png

Dalliance

Within Dalliance you have access to following:

  • ref_loc - Lists the genome reference being used and the current chromosome and location. You can change the location by entering either a start and end position or a single base position.
  • zoom - Control the zoom depth.
  • add_track - Adds a new track to the current view.
  • track_options - Modify track options such as the max depth, and colors.
  • print - Export current view as an SVG or PNG.
  • options - Change some of Dalliance’s options such as vertical guideline location, scrolling direction.

Snoopy

Variant Decisions

When either of the decision buttons are clicked, you will advance to the next variant.

  • not_a_variant - You are certain that the called site is not actually a variant.
  • uncertain - You are unsure if the called site is a variant.
  • variant - You are certain that the called variant is truly a variant.

Viewing

  • view - This dropdown button allows you to select four different track styles:
    • Raw - Display the bases with color scheme as specified in the settings.
    • Condensed - Only display a base if it differs from the reference. If a read exists and is in agreement with the reference, use match color as set in your settings.
    • Mismatch - Color code plus strand / minus strand if reference agreement exists. If a base differs, display with the base color as given in settings for raw.
    • Coverage - Presents a histogram of coverage. If more than 20% of the bases differ from reference, the proportion of bases are displayed with their bases colors.
  • snapshot - Clicking this will take a snapshot of whatever view is currently loaded into Dalliance.

Admin

  • restart - Stop and restart Snoopy button, there will be a prompt asking if you wish to save your progress.
  • save - Save whatever progress you have made so far. The output format is described in Saving Results.

Settings

View and change the following settings:

  • Connections
    • Default Remote, Local and SSH-Bridge settings (URL, credential requirements)
  • Dalliance zoom level
    • How deep should Dalliance be zoomed into after variant decision
  • Color settings
    • nucleotide bases colors
  • Mismatch style
    • Plus/minus strand colors
    • Show insertions
    • Reflect base quality with transparency
  • Condensed style
    • Match color
    • Reflect base quality with transparency
  • Coverage histogram style
    • Allele threshold (between 0 and 1): the minimum ratio of allele frequencies before a mismatch is displayed
    • Height
  • Snapshots
    • Automatically take snapshots at each variant

Help

A link to the documentation hosted on Read The Docs.

GitHub

A link to the GitHub repository holding the snoopy’s source code.