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About AutoQC

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Validation Checks

The QC system performs the following checks

Submission File

QC system checks the submission file to see if the data in it matches the specification as described in Submission File.

QC system also performs certain Pedigree Checks on the submission file such as -

  1. Do records for an individual identified as a parent exist in the submission file.
  2. Individuals identified as Fathers are males.
  3. Individuals identified as Mothers are Females.
  4. Ensure an individual's age is less than the age of his/her parents.
  5. Ensure an individual is not the same as his/her father/mother.
  6. Every family has at least one individual who is a Proband. (*unless submission disorder is indicated as "Control")

Phenotypic Data Files

The QC system checks to see if the data contained in each phenotypic data file matches the information contained in the corresponding data dictionary file.

Requirements

The QC system expects all phenotypic files submitted to have a first column as ind_id that matches the individual id ( ind_id column) in the submission file.

The QC system performs check such as:

  1. Ensures that all individuals mentioned in the phenotypic files have records in the submission file.
  2. Is data of the correct data type.
  3. Does data fall within the valid range of values.

Content Checks

The QC system checks that:

  1. Pairs of individual IDs (ind_id) and Sampled (formerly IBX) sample IDs (cell_id) in data submission match Sampled (formerly IBX) records
  2. DSM codes in extended diagnosis file (column code) are valid codes for the declared diagnostic system (dx_system).

Previous Validations

The Previous Validations list all prior workflows run by the user. The user can click on any of the previous runs to view results from that QC run.