Deleting Variants
The Scout command line provides instructions to remove variants from one or more cases using the scout delete variants
command.
Usage
To view available options, run:
scout delete variants --help
This will display:
Usage: scout delete variants [OPTIONS]
Delete variants for one or more cases.
Options:
-u, --user TEXT User running this command (email) [required]
-c, --case-id TEXT Case ID (e.g., expertpoodle or helpedgoat)
-f, --case-file PATH Path to file containing a list of case IDs
-i, --institute TEXT Restrict to cases with the specified institute ID
--status [prioritized|inactive|active|solved|archived|ignored]
Restrict to cases with the specified status
--older-than INTEGER Remove variants from cases older than (months)
--analysis-type [external|mixed|ogm|panel|panel-umi|unknown|wes|wgs|wts]
Restrict to cases with the specified analysis type
--rank-threshold INTEGER Remove only variants with a rank lower than this threshold
--variants-threshold INTEGER Remove variants only from cases containing at least this number of variants
--rm-ctg [cancer|cancer_sv|fusion|mei|outlier|snv|str|sv]
Remove only the specified variant categories
--keep-ctg [cancer|cancer_sv|fusion|mei|outlier|snv|str|sv]
Keep only the specified variant categories
--dry-run Perform a simulation without removing any variants
--help Show this message and exit.
Parameter Descriptions
Option | Description |
---|---|
--user (-u) |
Required. The email of the user executing the command. The user must exist in the Scout database. |
--case-id (-c) |
Optional. The case ID (e.g., expertpoodle or helpedgoat ). |
--case-file (-f) |
Optional. Path to a file containing a list of case IDs. |
--institute (-i) |
Optional. Institute ID. Not required if a case ID is provided. |
--status |
Optional. Restrict removal to cases with the specified status (e.g., solved ). |
--older-than |
Optional. Remove variants from cases older than the specified number of months (e.g., 12 for cases older than a year). |
--analysis-type |
Optional. Restrict removal to cases with the specified analysis type. |
--rank-threshold |
Optional. Remove only variants with a rank lower than this threshold. |
--variants-threshold |
Optional. Remove variants only from cases containing at least this number of variants. |
--rm-ctg |
Optional. Remove only the specified variant categories. Example: --rm-ctg snv --rm-ctg sv . |
--keep-ctg |
Optional. Keep only the specified variant categories. Cannot be used together with --rm-ctg . Use multiple times to specify more than one category. |
--dry-run |
Optional. Runs a simulation, showing an estimate of the number of variants to be removed without actually deleting anything. |
Note: If you are removing variants from Scout for the first time, it is strongly recommended to run a simulation first using the
--dry-run
option.
Example Command
To simulate the deletion of variants that:
- Have a rank lower than
5
- Belong to cases with
wgs
analysis type - Contain at least
100,000
variants - Are older than
24
months
Run:
scout delete variants --loglevel WARNING \
-u youremail \
--rank-threshold 5 \
--analysis-type wgs \
--variants-threshold 100000 \
--older-than 24 \
--dry-run