Snoopy Documentation¶

Manual¶

Quickly load a few files and start QC with little preparation.

In this mode, you select one-by-one a single set of sequence files (eg a single individual or a trio) and a list of candidate variant locations. Snoopy will then load the set of sequence files and visit each of the candidate variant locations.

Batch¶

Review several sets of sequence files.

In this mode, you can review several sets of sequence files (e.g. several sets of individuals or several different trios). As loading all of this information one-by-one with in the web interface would be cumbersome, the batch mode requires a JSON file which lists all of the sequence files and the variant locations. This file contains an array of sessions, where each session consists of:

• A set of sequence files (BAM, CRAM) which you want to view together at each of the locations in
• A list of variant locations (SNPs or CNVs) which you want to review in the sequence files.

For example, a session may consist of:

• a trio of sequence files mother.bam, father.bam, offspring.bam
• a set of de novo sites which need to be verified chr5:96244805, chr11:28483998, chr12:106799289, ...

Local Files¶

Remote Files¶

Summary¶

Variant List File¶

The variant text file can list both SNPs and CNVs. SNPs can be in any of the following formats:

chr:location
chr-location
chr,location
chr location

The format for CNVs is as SNPs except the location consists of two numbers. For example, a CNV location may be 16:start-end.

Batch JSON File¶

A JavaScript Object Notation (JSON) file is used to specify a set of sessions when using the batch mode of Snoopy. The idea is to use construct the JSON file with some scripting language (e.g. Python or Perl) rather than having to manually loading files. The general structure of the batch file is an array of sessions as follows:

sessions:
    session 1:
        variants: array of variant locations | a file listing variant locations
        sequence_files: array of sequence files (BAM or CRAM)
    session 2:
        variants: array of variant locations | a file listing variant locations
        sequence_files: array of sequence files (BAM or CRAM)
    .
    .
    .

In the JSON format:

{
    "sessions": [
        {
            "variants": [
                "chr-loc",
                "chr-loc",
                "chr-loc"
            ],
            "sequence_files": [
                "path/to/sequence file 1",
                "path/to/sequence file 2",
                "path/to/sequence file 3"
            ]
        },
        .
        .
        .
    ]
}

The format of the variants takes the form as that in the Variant List File section.

{
    "sessions": [
        {
            "variants": [
                "16-48000491",
                "16-48001121",
                "16-48001200"
            ],
            "sequence_files": [
                "/users/joe/examples/mother1.bam"
                "/users/joe/examples/father1.bam"
                "/users/joe/examples/offspring1.bam"
            ]
        },
        {
            "variants": [
                "12-18001",
                "12-1820491",
                "14-1803735",
                "15-1840848",
            ],
            "sequence_files": [
                "/users/joe/examples/individual.bam"
            ]
        }
    ]
}

Start local server¶

$ snoopy -l

Start local server at port 8888¶

$ snoopy -l -p 8888

Start SSH-Bridge with username bob at big-bio-server¶

$ snoopy -s bob@big-bio-server

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.