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The load config

Scout have the possibility to store loads of information about a case and the samples that are included. It is cumbersome to specify to many parameters on the command line so there is an option to give this information in a yaml formated config file. Here we can give scout some meta information about the analysis, how it was performed, information about family, samples etc.

The basic structure of a load config looks like:

owner: str(mandatory)

family: str(mandatory)
  - analysis_type: str(optional), [wgs,wes,panel,external]
    sample_id: str(mandatory)
    capture_kit: str(optional)
    father: str(mandatory)
    mother: str(mandatory)
    sample_name: str(mandatory)
    phenotype: str(mandatory), [affected, unaffected, unknown]
    sex: str(mandatory), [male, female, unknown]
    expected_coverage: int(mandatory)
    vcf2cytosure: str(optional) # path to CGH file
    bam_path: str(optional) # path to bam file
    rhocall_bed: str(optional) # path to bed file
    rhocall_wig: str(optional) # path to wig file
    upd_regions_bed: str(optional) # path to bed file
    upd_sites_bed: str(optional) # path to bed file
    tiddit_coverage_wig: str(optional) # path to wig file

    tissue_type: str(optional)
    tumor_type: str(optional)
    tmb: str(optional) # Tumor mutational burder [0,1000]
    msi: str(optional) # Microsatellite instability [0,60]
    tumor_purity: str(optional) # [0,1]

vcf_snv: str(optional)
vcf_sv: str(optional)
vcf_cancer: str(optional)
vcf_snv_research: str(optional)
vcf_sv_research: str(optional)
vcf_cancer_research: str(optional)

madeline: str(optional)

peddy_ped: str(optional)
peddy_ped_check: str(optional)
peddy_sex_check: str(optional)

multiqc: str(optional)

default_gene_panels: list[str](optional)
gene_panels: list[str](optional)

# ATM rare or cancer
track: list[str][optional]

# meta data
rank_model_version: str(optional)
sv_rank_model_version: str(optional)
rank_score_threshold: float(optional)
analysis_date: datetime(optional)
human_genome_build: str(optional)

Let's go through each field:

  • owner each case has to have a owner, this refers to an existing institute in the scout instance
  • family each case has to have a family id
  • samples list of samples included in the case

    • analysis_type specifies the analysis type for the sample
    • samlple_id identifyer for a sample
    • capture_kit for exome specifies the capture kit
    • father sample id for father or 0
    • mother sample id for mother or 0
    • phenotype specifies the affection status of the sample in human readable format
    • sex specifies the sex of the sample in human readable format
    • expected_coverage the level of expected coverage
    • bam_file Path to bam file to view alignments
    • rhocall_bed Path to bed file to view alignments (Reference)[]
    • rhocall_wig Path to wig file to view alignments (Reference)[]
    • upd_regions_bed Path to bed file to view alignments (Reference)[]
    • upd_sites_bed Path to bed file to view alignments (Reference)[]
    • tiddit_coverage_wig Path to wig file to view alignments (Reference)[]
    • vcf2cytosure Path to CGH file to allow download per individual
    • tumor_type Type of tumor
    • tissue_type What tissue the sample originates from
    • tmb Tumor mutational burden
    • msi Microsatellite instability
    • tumor_purity Purity of tumor sample
  • vcf_snv path to snv vcf file

  • vcf_sv
  • vcf_snv_research path to vcf file with all variants
  • vcf_sv_research
  • vcf_cancer
  • vcf_cancer_research
  • madeline path to a madeline pedigree file in xml format
  • peddy_ped path to a peddy ped file with an analysis of the pedigree based on variant information
  • peddy_ped_check path to a peddy ped check file
  • peddy_sex_check path to a peddy ped check file
  • multiqc path to a multiqc report with arbitrary information
  • default_gene_panels list of default gene panels. Variants from the genes in the gene panels specified will be shown when opening the case in scout
  • gene_panels list of gene panels. This will specify what panels the case has been run with
  • rank model version which rank model that was used when scoring the variants
  • SV rank model version the SV rank model version used when scoring SV variants
  • rank_score_treshold only include variants with a rank score above this treshold
  • analysis_date time for analysis in datetime format. Defaults to time of uploading
  • human_genome_build what genome version was used.

Minimal config

Here is an example of a minimal load config:


owner: cust004

family: '1'
  - analysis_type: wes
    sample_id: NA12878
    capture_kit: Agilent_SureSelectCRE.V1
    father: 0
    mother: 0
    sample_name: NA12878
    phenotype: affected
    sex: male
    expected_coverage: 30

vcf_snv: scout/demo/643594.clinical.vcf.gz

CGH (vcf2cytosure) for download

By giving a path to each individual vcf2cytosure-file these are made available for download on the case page. Such SV files can be visualized using standard arrayCGH analysis tools. See vcf2cytosure.