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 Jobsfrom the left navigation tab underneath
Cohorts, and click the
Import Filesbutton. The
Import Filesbutton is also available under the
Data Setsleft navigation item.
Data Setmenu item is used to view imported data sets and information. The
Import Jobsmenu 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.Choose a data type among
- Copy Number Variation
- 2.Choose a new study name by selecting the radio button:
Create new studyand entering a
- 3.To add new data to an existing Study, select the radio button:
Select from list of studies* and select an existingStudy Name` from the dropdown.
- 4.To add data to existing records or add new records, select
- 5.To replace data, select
Replace. If you are ingesting data again, use the Replace job type.
- 6.Enter a
- 7.The Cohorts metadata model will be selected by default.
- 9.Navigate to VCFs located in the Project Data.
- 10.Select each single-sample VCF or multi-sample VCF to ingest.
JSON for VCF are both compatible formats for variant data ingestion.
- 2.Navigate to the metadata (phenotype) data tsv in the project Data.
- 3.Select the TSV file or files for ingestion.
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
sampleslisted in the header need to match the metadata files.
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.