The validation tool is crafted to verify if the selected summary statistics files adhere to the gwas-ssf schema defined by the GWAS catalog. This documentation serves as a guide on utilizing the gwas-ssf validate command in your terminal environment.
gwas-ssf validate file [options]
| Options | short name | type | Default value | Description |
|---|---|---|---|---|
--help |
-h |
Boolean | False | Display help message, providing guidance on how to use the tool and its various functionalities. |
--errors-out |
-e |
Boolean | False | Output errors to a CSV file, <filename>.err.csv.gz |
--p-zero |
-z |
Boolean | False | Force p-values of zero to be allowable. Takes precedence over inferred value (-i) |
--min-rows |
-m |
int | 100,000 | Minimum rows acceptable for the file |
--chunksize |
-s |
int | 1,000,000 | Number of rows to store in memory at once. Increase this number for more speed at the cost of more memory. Decrease to save memory, at the cost of speed |
--infer-from-metadata |
-i |
Boolean | False | Infer validation options from the metadata file <filename>-meta.yaml. E.g. fields for analysis software and negative log10 p-values affect the data validation behaviour. |
Suppose you have a file named GCST12345_formatted.tsv that needs to be validated to see if it adheres to the GWAS-SSF schema.
In your file, encountering a p-value of 0 can cause validation failure. However, we make exceptions for 0 p-values if the analysis software is provided in the metadata.
Option 1: Force to allow zero P-values
gwas-ssf validate GCST12345_formatted.tsv --p-zero --errors-out GCST12345_formatted.errOption 2: Verify analysis software field in the metadata YAML file
gwas-ssf validate GCST12345_formatted.tsv --infer-from-metadata --errors-out GCST12345_formatted.errIn your file, encountering fewer than 100,000 variants (rows) can lead to validation failure. However, we do accept data with lower row numbers under certain circumstances (please contact [email protected] to request an eligibility review). To bypass the minimum row number requirement, and enable you to validate the rest of the file, utilize the --min-rows option.
gwas-ssf validate GCST12345_formatted.tsv --errors-out GCST12345_formatted.err --min-rows 50000Copyright © EMBL-EBI 2024 | EMBL-EBI is an Outstation of the European Molecular Biology Laboratory | Terms of use | Data Preservation Statement