Import New Samples

ICA Cohorts can pull any molecular data available in an ICA Project, as well as additional sample- and subject-level metadata information such as demographics, biometrics, sequencing technology, phenotypes, and diseases.
To import a new data set, select Import Jobs from the left navigation tab underneath Cohorts, and click the Import Files button. The Import Files button is also available under the Data Sets left navigation item.
The Data Set menu item is used to view imported data sets and information. The Import Jobs menu item is used to check the status of data set imports.
Confirm that the project shown is the ICA Project that contains the molecular data you would like to add to ICA Cohorts.
  1. 1.
    Choose a data type among
    • Germline
    • Somatic
    • Copy Number Variation
  2. 2.
    Choose a new study name by selecting the radio button: Create new study and entering a Study Name.
  3. 3.
    To add new data to an existing Study, select the radio button: Select from list of studies* and select an existing Study Name` from the dropdown.
  4. 4.
    To add data to existing records or add new records, select Job Type, Append.
  5. 5.
    To replace data, select Job Type, Replace. If you are ingesting data again, use the Replace job type.
  6. 6.
    Enter a Study description.
  7. 7.
    The Cohorts metadata model will be selected by default.
  8. 8.
    Click Next.
  9. 9.
    Navigate to VCFs located in the Project Data.
  10. 10.
    Select each single-sample VCF or multi-sample VCF to ingest.
JSON for VCF are both compatible formats for variant data ingestion.
  1. 1.
    Click Next.
  2. 2.
    Navigate to the metadata (phenotype) data tsv in the project Data.
  3. 3.
    Select the TSV file or files for ingestion.
  4. 4.
    Click Finish.
The sample identifiers used in the VCF columns need to match the sample identifiers used in subject/sample metadata files; accordingly, if you are starting from JSON files containing variant- and gene-level annotations provided by ILMN Nirvana, the samples listed in the header need to match the metadata files.

Metadata and File Types

Project name
The ICA project for your cohort analysis (cannot be changed.)
Study name
Create or select a study. Each study represents a subset of data within the project.
Short description of the data set (optional).
Job type
Append: Appends values to any existing values. If a field supports only a single value, the value is replaced.
Replace: Overwrites existing values with the values in the uploaded file.
Subject metadata files
Subject metadata file(s) in tab-delimited format. For Append and Replace job types, the following fields are required and cannot be changed: - Sample identifier - Sample display name - Subject identifier - Subject display name - Sex
Note: If annotating large sets of samples with molecular data, expect the annotation process to take over 20 minutes per whole genome sample. You will receive an email both when your ingestion begins and when it is complete.