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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.