Prepare Metadata Sheets
In ICA Cohorts, metadata describe any subjects and samples imported into the system in terms of attributes, including:
- demographics such as age, sex, ancestry;
- phenotypes and diseases;
- biometrics such as body height, body mass index, etc.;
- pathological classification, tumor stages, etc.;
- family and patient medical history;
- sample type such as FFPE,
- tissue type,
- sequencing technology: whole genome DNA-sequencing, RNAseq, single-cell RNAseq, among others.
A metadata sheet will need to contain at least these four columns per row:
- Subject ID - identifier referring to individuals; use the column header "SubjectID".
- Sample ID - identifier for a sample. Sample IDs need to match the corresponding column header in VCF/GVCFs; each subject can have multiple samples, these need to be specified in individual rows for the same SubjectID; use the column header "SampleID".
- Biological sex - can be "Female (XX)", "Female", or simply "F"; "Male (XY)", "Male", "M"; "X (Turner's)"; "XXY (Klinefelter)"; "XYY"; "XXXY" or "Not provided". Use the column header "DM_Sex" (demographics).
- Sequencing technology - can be "Whole genome sequencing", "Whole exome sequencing", "Targeted sequencing panels", or "RNA-seq"; use the column header "TC" (technology).