Reference: Samplesheet schema
Contents
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 |
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Validates the JSON representation of a samplesheet |
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type |
array |
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items |
type |
object |
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properties |
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Sampleset name must be provided and cannot contain spaces |
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type |
string |
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pattern |
^\S+$ |
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VCF path must end with .vcf.gz, mutually exclusive with other formats |
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type |
string |
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pattern |
^\S+\.vcf\.gz$ |
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anyOf |
type |
string |
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pattern |
^\S+\.vcf\.gz$ |
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type |
string |
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maxLength |
0 |
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minLength |
1 |
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|
Specify whether to import genotypes (default: GT), or imputed dosages (DS) from the VCF file. |
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anyOf |
type |
string |
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pattern |
/^(GT|DS)$/ |
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type |
null |
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|
Plink 1 binary fileset prefix, must not end with bed / bim / fam, mutually exclusive with other formats |
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anyOf |
type |
string |
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pattern |
^(?!vcf$|vcf\.gz$|bim$|bed$|fam$)[^.]+$ |
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type |
string |
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maxLength |
0 |
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minLength |
1 |
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|
Plink 2 binary fileset prefix, must not end with pvar / pgen / psam, mutually exclusive with other formats. Must not be zstd compressed. |
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anyOf |
type |
string |
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pattern |
^(?!vcf$|vcf\.gz$|psam$|pvar$|pgen$)[^.]+$ |
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type |
string |
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maxLength |
0 |
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minLength |
1 |
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|
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. |
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anyOf |
type |
null |
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type |
string |
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dependencies |
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|
allOf |
not |
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not |
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|
allOf |
not |
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not |
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|
allOf |
not |
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not |
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minItems |
1 |
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uniqueItems |
True |
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