Comments (3)
This sounds great for the delivery report.
from chanjo2.
This is great, thanks! I will incorporate it into the raredisease delivery report.
from chanjo2.
Hello again @peterpru, I've just merged the new feature and I'm going to create and deploy on cg-vm1 a new release of chanjo2 today.
Here's an example of the query you need to send from cg (you can also try it from the terminal):
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": "/home/proj/stage/housekeeper-bundles/safeguinea/2023-06-26/ADM997A3_lanes_12_sorted_md.d4"
}
],
"hgnc_gene_ids": [
2861, 3791, 6481, 7436, 30521
],
"coverage_threshold": 10,
"interval_type": "genes"
}'
from chanjo2.
Related Issues (20)
- On report page, add one more field to specify a list of completeness cutoffs for the stats HOT 1
- Completeness cutoff on report has no memory of submitted form when page is refreshed
- Js errors on report page
- Lib import error while connecting to MySQL using MacOS HOT 1
- Failed to load API definition for Chanjo2 API HOT 7
- On report page, customize search to allow also HGNC symbols and Ensembl IDs
- Server timeout when loading exons HOT 13
- Trouble getting /report calls to the correct end point, round 2 HOT 4
- Modify report endpoints to only accept forms and not json data? HOT 6
- Detailed gene info in main report HOT 2
- Issues with customizing report through gene panel name HOT 3
- Occasionally large differences in coverage for same gene region in same sample HOT 11
- Can't install mysqlclient on macOS
- Warnings by the black (lint) action
- Startup errors crashing in log statement HOT 17
- Address security alerts
- Improve performance of get_coverage_completeness.py HOT 5
- Clarify "Average coverage" HOT 2
- Handle errors for condensed stats endpoint
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