coyote3

Complete Click Paths

This chapter gives concrete click-by-click operating paths.

A. Process a new DNA sample to report

1. Open /samples/live.
2. Find sample and click sample ID.
3. You are on /dna/sample/<sample_id>.
4. Review filter panel and active gene filters.
5. Open sample settings from gear icon if ISGL/ad-hoc update is needed.
6. Return to DNA page and review SNVs.
7. Click a variant row to open /dna/<sample_id>/var/<var_id>.
8. Apply classification and comments.
9. Return to list and repeat for key variants.
10. Review CNV/translocation sections if present for assay.
11. Click report preview action (/dna/sample/<sample_id>/preview_report).
12. Validate content, then save (/dna/sample/<sample_id>/report/save).
13. Return to /samples and verify sample is in done/reported.

B. Process RNA sample

1. Open /samples/live.
2. Click RNA sample.
3. You are on /rna/sample/<sample_id>K=.
4. Review fusion candidates and thresholds.
5. Open each fusion (/rna/fusion/<fusion_id>).
6. Mark FP where needed.
7. Add summary/sample comments.
8. Generate preview (/rna/sample/preview_report/<sample_id>).
9. Generate/export PDF (/rna/sample/report/pdf/<sample_id>).

C. Review historical reported occurrences of a variant

1. From variant detail or list, open history link.
2. Route opens /reported_variants/variant/<variant_id>/<tier>.
3. Review which samples/reports contain that reported variant identity.
4. Open linked sample/report for context.

D. Perform global annotation search

1. Open /search/tiered_variants.
2. Select search mode (gene/variant/etc.).
3. Enter query and optionally assay filter.
4. Include annotation text if needed.
5. Review returned annotation docs and linked samples/reports.

E. Edit sample gene constraints

1. Open /samples/<sample_id>/edit.
2. Load ISGL list from available options.
3. Apply selected ISGL entries.
4. Add ad-hoc genes if case requires targeted list.
5. Verify effective genes count/list.
6. Return to DNA page and continue review.

F. Retrieve previously saved report

1. Open /samples/done.
2. Find sample and report row.
3. Click report link to view: /samples/<sample_id>/reports/<report_id>.
4. Click download icon/link for attachment route if needed.

G. When to use which page

• Use /samples for workload and navigation.
• Use /dna/... or /rna/... for interpretation actions.
• Use /search/tiered_variants for cross-sample annotation discovery.
• Use /reported_variants/... for report-time occurrence history.
• Use /admin/... only for governance/configuration changes.

H. Use MATRIX for cross-panel gene discovery

1. Open /assay-catalog-matrix.
2. Search for target gene.
3. Compare presence across modality/category/list columns.
4. Note the relevant modality/category/list.
5. Open /assay-catalog for detailed metadata and export.

I. Use CATALOG for drill-down and export

1. Open /assay-catalog.
2. Select modality in left tree.
3. Select category (and list if needed).
4. Use gene search box in right table.
5. Export genes using CSV action for the current view.

J. Use VARIANT SEARCH for historical context

1. Open /search/tiered_variants.
2. Enter search string.
3. Select search mode (variant/gene/transcript/subpanel/author).
4. Optionally select assay groups.
5. Enable annotation text when broader context is needed.
6. Review linked samples and reports in results.

Related guide:

• Navbar Tools: Matrix, Catalog, and Variant Search

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