Data intake formats

Intake formats for typical file types of a typical cancer genomic study

Somatic SNV/indel should be in VCF or tabular format with following fields:

• chromosome
• 1-based (vcf) or 0-based (tabular) position
• reference allele
• mutant allele
• DNA sequencing read count per allele
• RNAseq read count per allele (will be great if this can be available for cases with RNAseq)
• sample name

SV and Fusion should be a tabular format with following fields:

• chromosome A
• 0-based position A
• strand A, value is + or -
• chromosome B
• 0-based position B
• strand B
• Sample name

CNV should be a tabular format with following fields:

• chromosome
• 0-based start position
• 0-based stop position
• Magnitude of change, can be in log2(tumor/germline), or seg.mean etc. We need a consistent quantification for all CNV calls

Gene expression, for both FPKM/TPM and raw counts should be a tabular gene-by-sample value matrix:

• Genes on rows, samples on columns
• Please use either HGVS symbol or GENCODE gene accession as gene names

tSNE results based on bulk transcriptome or methylome should be a tabular file:

• has a header row
• has columns for sample and X/Y coordinates

Clinical data can be in a tabular matrix with samples and variables on rows or columns.

• When variables are on columns, there should be a row called DATATYPE to identify data type of each column. Supported values are "categorical", "integer", "float"
• likewise, when variables are on rows, the DATATYPE should be a column
• For variables identified as numeric, non-numeric values will be treated as exceptions

Survival data should be a tabular matrix with following columns

• Sample name
• Time to event in decimal years
• Exit code, 0=alive, 1=dead
• (Additional columns for time to event and exit code could be added when more types of survival data are available)

Single-cell RNAseq TBA