User Interface

When reviewing variants you’ll have the following view:

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

Dalliance

Within Dalliance you have access to following:

• - 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.
• - Control the zoom depth.
• - Adds a new track to the current view.
• - Modify track options such as the max depth, and colors.
• - Export current view as an SVG or PNG.
• - 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.

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

Navigation

• - This displays the current variant and a QC decision, if available. If you click this button you will presented with a window which summarizes all of the QC decisions made so far, as well as allowing you to quickly navigate to a different variant.
• - Returns to the current variant of interest if you’ve dragged the Dalliance track away.
• - Go to the previous variant. Clicking this button does not register any variant decisions.

Viewing

• - 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.

• - Clicking this will take a snapshot of whatever view is currently loaded into Dalliance.

Admin

• - Stop and restart Snoopy button, there will be a prompt asking if you wish to save your progress.
• - 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.