Metadata Provided
Each data request includes a text file called SAMPLE_INFO.txt
that provides a number of file level properties (sample identifiers, clinical attributes, etc). The following is a list of properties provided.
Property | Description |
---|---|
file_path | The path to the file in your St. Jude Cloud project. |
subject_name | A unique subject identifier assigned internally at St. Jude. |
sample_name | A unique sample identifier assigned internally at St. Jude. |
sample_type | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft |
sequencing_type | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. |
file_type | One of BAM, CNV, gVCF, Somatic_VCF |
description | Optional field that may contain additional file information. |
j_diseases | Short disease identifier used internally at St. Jude. When determining primary diagnosis, use attr_diagnosis instead! |
sj_datasets | If present, the datasets in the data browser which this file is associated with. |
sj_pmid_accessions | If the file was associated with a paper, the related Pubmed accession number. |
sj_ega_accessions | If the file was associated with a paper, the related EGA accession number. |
attr_age_at_diagnosis | Age at first diagnosis (normalized as a decimal value). |
attr_diagnosis | Primary diagnosis. |
attr_ethnicity | Self-reported ethnicity according to the US Census Bureau classifications. |
attr_race | Self-reported race according to the US Census Bureau classifications. |
attr_sex | Self-reported sex. |
sj_dataset_accession | If present, the permanent accession number assigned in St. Jude Cloud. |
sj_embargo_date | The embargo date, which specifies the first date which the files can be used in a publication. |