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Docs for the new coverage condensed summary endpoint #322

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merged 2 commits into from
Jun 20, 2024
Merged

Docs for the new coverage condensed summary endpoint #322

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e5aae85
Better endpoint
Jun 20, 2024
a8f69a6
Fix sample name
Jun 20, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
## [unreleased]
### Added
- Condensed `/coverage/d4/genes/summary` for condensed stats over a gene list
- Documentation for new coverage summary endpoint
### Changed
- GitHub tests action to use d4tools 0.3.10
### Fixed
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38 changes: 37 additions & 1 deletion docs/usage/sample-coverage.md
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Expand Up @@ -130,6 +130,42 @@ And it would return the following result:
]
```

### Condensed summary stats for one or more samples over a list of HGNC IDs

To obtain condensed statistics for one or more samples, use the `/coverage/d4/genes/summary` endpoint.
Send a request with a list of HGNC gene IDs, the path to the d4 files for the samples, and the coverage threshold for computing coverage completeness.
The endpoint will return the average coverage and coverage completeness for all the genes included in the query.
You need to provide a parameter `interval_type` to specify whether the statistics should be computed over entire genes, gene transcripts, or exons.

#### Request example:

``` shell
curl -X 'POST' \
'https://chanjo2-stage.scilifelab.se/coverage/d4/genes/summary' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{
"build": "GRCh37",
"samples": [
{
"name": "TestSample",
"coverage_file_path": "<path-to-d4-file.d4>"
}
],
"hgnc_gene_ids": [
2861, 3791, 6481, 7436, 30521
],
"coverage_threshold": 10,
"interval_type": "genes"
}'
```

#### Response from chanjo2:

``` shell
{"TestSample":{"mean_coverage":54.38,"coverage_completeness_percent":33.03}}
```

### Case and samples coverage queries

Genes, transcripts and exons coverage data can be computed by sending POST requests to their relative endpoints:
Expand All @@ -150,7 +186,7 @@ These endpoints are very similar and accept the following parameters:

While the only required parameter is "build", <strong>it is necessary to specify a list of genes</strong> (either ensembl_gene_ids, hgnc_gene_ids or hgnc_gene_symbols) and either <strong>a case or a list of samples</strong>.

### Coverage and coverage completeness query esamples
### Coverage and coverage completeness query examples

- Given all samples from case "internal_id", retrieve mean coverage and coverage completeness with threshold 30, 20 on the genes from the Cerebral folate deficiency PanelAPP panel (*DHFR, FOLR1, MTHFR, SLC46A1*):

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