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Loading Scout

Institute

To load a institute into scout use the command scout load institute. As mentioned in the user guide an institute has to have a unique internal id, this is specified on the command line with -i/--internal-id. Also a display name could be used if there is a need for that, specify with -d/--display-name. If no display name is choosen it will default to internal id. Note that internal id is unique.

User

To load a user into scout use the command scout load user. A user has to:

  • belong to an institute
  • have a name
  • have a email adress

An example could look like:

scout load user --institute-id cust000 --user-name "Clark Kent" --user-mail clark@mail.com

Case

When loading a case into scout it is possible to use either a config file or to specify parameters on the command line.

Scout Load Config

The loading config is a .yaml file and can include all the necessary information to scout. Command line options will overload information in the config file. For a complete spec of the config file see load config

An example file, (this file is located in scout/demo/643594.config.yaml):

---

owner: cust000

family: '643594'
samples:
  - analysis_type: wes
    sample_id: ADM1059A2
    capture_kit: Agilent_SureSelectCRE.V1
    father: ADM1059A1
    mother: ADM1059A3
    sample_name: NA12882
    phenotype: affected
    sex: male
    expected_coverage: 30
  - analysis_type: wes
    sample_id: ADM1059A1
    capture_kit: Agilent_SureSelectCRE.V1
    father: '0'
    mother: '0'
    sample_name: NA12877
    phenotype: unaffected
    sex: male
    expected_coverage: 30
  - analysis_type: wes
    sample_id: ADM1059A3
    capture_kit: Agilent_SureSelectCRE.V1
    father: '0'
    mother: '0'
    sample_name: NA12878
    phenotype: unaffected
    sex: female
    expected_coverage: 30

vcf_snv: scout/demo/643594.clinical.vcf.gz
vcf_sv: scout/demo/643594.clinical.SV.vcf.gz
vcf_snv_research: scout/demo/643594.research.vcf.gz
vcf_sv_research: scout/demo/643594.research.SV.vcf.gz

madeline: scout/demo/madeline.xml
default_gene_panels: [panel1]
gene_panels: [panel1]

# meta data
rank_model_version: '1.12'
rank_score_threshold: -100
analysis_date: 2016-10-12 14:00:46
human_genome_build: 37

Load case from CLI without config

Cases can be loaded without config file, in that case the user needs to specify a ped file and optionally one or several VCF files. An example could look like

scout load case --ped path/to/file.ped --vcf-snv path/to/file.vcf

Please use

scout load case --help

for more instructions