Reference: Samplesheet schema

The documentation below is automatically generated from the schema. The JSON file contains additional technical detail not shown in the table below. See How to set up a samplesheet for a user-friendly step-by-step introduction to the genotype inputs.

Each row in a samplesheet can only have a single genomic data format (i.e. they are mutually exclusive). This reference is helpful if you want to:

• Use the JSON input format (instead of CSV samplesheets) and validate the structure of your JSON

• Deeply understand samplesheet data structure

But this schema probably isn’t very helpful for most users, so it’s OK to ignore it!

Target genome schema

https://raw.githubusercontent.com/pgscatalog/pgsc_calc/dev/assets/schemas/samplesheet.json
Validates the JSON representation of a samplesheet
type	array
items	type	object
	properties
	sampleset	Sampleset name must be provided and cannot contain spaces or reserved characters (‘_’ or ‘.’)
		type	string
		pattern	^[a-zA-Z0-9]*$
	path	A list of resolved target genome file paths
		type	array
		items	type	string
		maxItems	3
		minItems	1
		uniqueItems	True
	chrom	Specify the chromosome of associated genotyping data (must be in {1-22, X, XY, Y}). If all chromosomes are in the associated file (e.g. your data is not split by chromosome), set to null.
		type	null / string
		minLength	1
	format	Target genome data format.
		type	string
		enum	pfile, bfile, vcf
	vcf_genotype_field	Specify whether to import genotypes (default: GT), or imputed dosages (DS) from the VCF file.
		type	boolean
minItems	1
uniqueItems	True