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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