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.

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/target_genomes.json

Validates the JSON representation of a samplesheet

type

array

items

type

object

properties

  • sampleset

Sampleset name must be provided and cannot contain spaces

type

string

pattern

^\S+$

  • vcf_path

VCF path must end with .vcf.gz, mutually exclusive with other formats

type

string

pattern

^\S+\.vcf\.gz$

anyOf

type

string

pattern

^\S+\.vcf\.gz$

type

string

maxLength

0

minLength

1

  • bfile_path

Plink 1 binary fileset prefix, must not end with bed / bim / fam, mutually exclusive with other formats

anyOf

type

string

pattern

^(?!vcf$|vcf\.gz$|bim$|bed$|fam$)[^.]+$

type

string

maxLength

0

minLength

1

  • pfile_path

Plink 2 binary fileset prefix, must not end with pvar / pgen / psam, mutually exclusive with other formats. Must not be zstd compressed.

anyOf

type

string

pattern

^(?!vcf$|vcf\.gz$|psam$|pvar$|pgen$)[^.]+$

type

string

maxLength

0

minLength

1

  • 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 an empty string.

anyOf

type

null

type

string

dependencies

  • pfile_path

allOf

not

not

  • bfile_path

allOf

not

not

  • vcf_path

allOf

not

not

minItems

1

uniqueItems

True