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.
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 email@example.com
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
--- 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 bam_path: path/to/bam 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 bam_path: path/to/bam 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 bam_path: path/to/bam 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' sv_rank_model_version: '1.5' 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
scout load case --help
for more instructions