coyote3

DNA Workflow

This chapter documents the full DNA analyst workflow, including what happens after each user action.

Related diagrams:

• Flow Diagrams (DNA, RNA, Sample, Admin)

Entry point

• /dna/sample/<sample_id>

What loads when the page opens

When you open a DNA sample, Coyote3:

1. Loads sample, assay config, and schema.
2. Resolves assay group and subpanel.
3. Merges sample filters with assay defaults.
4. Builds effective gene set from ASP (Assay Specific Panel) genes + selected ISGL (In Silico Gene List) + ad-hoc genes.
5. Builds SNV query and loads variants.
6. Adds blacklist flags and global annotation/tier data.
7. Loads other enabled sections from assay config:
   • CNV
   • TRANSLOCATION
   • BIOMARKER
   • FUSION (if configured)

DNA list page sections

Typical sections on list_variants_vep.html:

• SNV list.
• CNV list.
• Translocation list.
• Optional biomarkers/fusions sections.
• Summary/comments area.
• Coverage links and report preview action.

Filters and sample settings behavior

On the DNA list page:

• Changing filters updates sample filter state.
• Reset returns filters to assay defaults.
• ISGL/ad-hoc settings from sample settings page immediately affect effective gene filtering.

Important behavior:

• Sample filters are mutable state on the sample.
• Later sessions see the latest saved filter values.

Variant-level actions

Open variant detail:

• /dna/<sample_id>/var/<var_id>

Available actions on variant detail:

• classify tier (/classify)
• remove classification (/rmclassify)
• mark/unmark false positive (/fp, /unfp)
• mark/unmark interesting (/interest, /uninterest)
• mark/unmark irrelevant (/irrelevant, /relevant)
• add blacklist flag (/blacklist)
• add comments and hide/unhide comments

Bulk actions

Route:

• POST /dna/<sample_id>/multi_class

Bulk actions can apply/remove:

• tiers (class docs plus text docs created in bulk path)
• false-positive flags
• irrelevant flags

CNV actions

CNV detail route:

• /dna/<sample_id>/cnv/<cnv_id>

Common CNV actions:

• mark/unmark interesting
• mark/unmark false-positive
• mark/unmark noteworthy
• hide/unhide CNV comments

Translocation actions

Translocation detail route:

• /dna/<sample_id>/transloc/<transloc_id>

Common translocation actions:

• mark/unmark interesting
• mark/unmark false-positive
• hide/unhide translocation comments

Auto-tier behavior while reviewing

When variants are shown, Coyote3 checks annotation history and chooses latest matching classification.

Matching priority:

1. HGVSp
2. HGVSc
3. genomic identity (CHR:POS:REF/ALT)

Scoping:

• solid: assay + subpanel scoped.
• other assay groups: assay scoped.

If no direct scoped class is found, additional classification lookup may provide assay-scoped fallback.

Report preview and save

Preview:

• /dna/sample/<sample_id>/preview_report

Save:

• /dna/sample/<sample_id>/report/save

Both use the same payload builder, so preview and saved report content are aligned.

Save path also persists:

• report file on disk
• samples.reports[] metadata and report_num
• immutable reported_variants snapshot rows

Practical productive workflow

1. Start from /samples/live.
2. Open sample and confirm assay/subpanel context.
3. Validate effective genes before deep review.
4. Tier only after reviewing existing global annotations and assay/subpanel fit.
5. Add concise interpretation comments.
6. Preview report and verify sections.
7. Save report and verify sample appears in done/reported list.

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