Submitting summary statistics only
For publications that are already included in the GWAS Catalog, we provide a partially pre-filled submission form showing each study (i.e. each GWAS analysis) in the publication. You will need to add information describing the corresponding summary statistics file for each study.
Please note, the pre-filled form should contain one row for each GWAS analysis in your publication, including one row for each set of summary statistics (i.e. each full set of p-values) that you have uploaded. For example, if you performed GWAS analyses for 100 different metabolite measurements, there should be 100 rows - one for each metabolite. If there are not enough rows to represent all of the GWAS analyses in your publication and/or the number of uploaded summary statistics, please contact gwas-subs@ebi.ac.uk for assistance.
Most studies submitted to the GWAS Catalog are for SNP-based analyses. If you would also like to submit gene-based or CNV-based summary statistics, please see https://www.ebi.ac.uk/gwas/apps/beyond-snps/.
Instructions are provided below. When you have completed the submission form, continue to upload the submission form in the Submission App.
Pre-filled data
Three columns have been filled in for you.
| Column header | Information provided | Example |
|---|---|---|
| Study accession | The GWAS Catalog study accession, beginning with “GCST” | GCST007280 |
| Reported trait | The trait under investigation | Reticulocyte count |
| Discovery sample | A description of the discovery sample (including number and ancestry) | 1,000 European ancestry cases, 1,000 European ancestry controls |
Data for you to enter
There are 14 empty columns for you to fill in. Mandatory columns are highlighted in orange in the submission form. Grey columns are optional. However, we encourage you to submit as much information as you can.
Do not upload a separate README file to Globus. Copy the contents of your README into the Readme text column of the submission form. The contents are stored as author notes in the metadata YAML. If you enter only README.txt, the author notes will contain only README.txt.
| Header | Description | Mandatory | Validation | Example |
|---|---|---|---|---|
| Study tag | Each genome-wide association study in the submission must have a unique free-text label. You can use any string of characters that will help you identify each individual GWAS. | yes | Free text | WHR_unadj |
| Genotyping technology | Method(s) used to genotype variants in the discovery stage. Separate multiple methods by pipes "|". | yes | Must match one of the following options:; Genome-wide genotyping array; Targeted genotyping array; Exome genotyping array; Whole genome sequencing; Exome-wide sequencing | Genome-wide genotyping array |
| Analysis software | Software and version used for the association analysis. | yes if any p-values in sumstats file = 0 | Free text | PLINK 1.9 |
| Imputation panel | Panel used for imputation | no | Free text | 1000 Genomes Phase 3 |
| Imputation software | Imputation software | no | Free text | IMPUTE |
| Variant count | The number of variants analysed in the discovery stage (after QC) | yes | Number >100,000 | 500000 |
| Adjusted covariates | Any covariates the GWAS is adjusted for. Multiple values can be listed separated by '|'. | no | Free text | age|sex |
| Summary statistics file | The name of the summary statistics file uploaded via Globus. Summary statistics must be submitted for at least one study. Enter "NR" for any additional studies without summary statistics. | yes | A valid filename | example.tsv |
| md5 sum | The md5 checksum of the summary statistics file. Must be entered for all studies with summary statistics. Enter "NR" for any studies without summary statistics. See how to calculate checksums here. | yes | A valid md5 checksum (32-digit hexadecimal number) | 49ea8cf53801c7f1e2f11336fb8a29c8 |
| Readme text | Author notes to accompany your analysis. Please copy notes into this cell directly, rather than uploading a separate readme file. If the same note applies to all studies in the submission, please copy the text into each row. Leave blank for any studies without summary statistics. | no | Standard readme text | See readme instructions here. |
| Summary statistics assembly | Genome assembly for the summary statistics. Must be entered for every row that includes summary statistics. Enter "NR" for any additional studies without summary statistics. | yes | Must match one of the following options:; GRCh38; GRCh37; NCBI36; NCBI35; NCBI34 | GRCh38 |
| Neg Log10 p-values | Enter yes if the summary statistics p-values are given in the negative log10 form. | no | Must match one of the following options:; Yes; No | yes |
| MAF lower limit | Lowest possible allele frequency given in summary statistics * | no | numeric | 0.0001 |
| Cohort(s) | List of any named cohort(s) represented in the discovery sample, separated by pipes "|". Enter only if the specific named cohorts are used in the analysis. | no | Free text | UKB|FINRISK |
| Cohort specific reference | List of any cohort specific identifier(s) issued to this research study, separated by pipes "|". For example, an ANID issued by UK Biobank. Please include the name of the cohort as a prefix. | no | Free text | UKB_ANID45956 |
| Sex | To indicate a sex-stratified analysis, enter the sex of participants as M or F. For non-sex-stratified analyses enter "combined", or NR if unknown. | no | Free text | combined |
| Coordinate system | Coordinate system used for the summary statistics: 1-based or 0-based (More info). | yes | Free text | 1-based |
* Effect allele frequency is a mandatory field. However, where privacy concerns might otherwise be a barrier to sharing the data (e.g. in small cohorts with sensitive phenotypes), a cutoff may be specified so that allele frequencies below that cutoff are rounded-up to mask their true values. For example, 0.01 here indicates the lowest possible value for the minor allele frequency in this file is 0.01, and anything below this threshold has been rounded up to 0.01 (noting that the minor allele is not necessarily the effect allele). Since masking allele frequency limits the downstream utility of the data, please submit full EAF data where possible.
Additional information
What if I can’t tell which study is which?
If you need more information to identify each study, you can find additional details at the GWAS Catalog website, on the relevant publication page (https://www.ebi.ac.uk/gwas/ + the PMID of the publication).
What if the prefilled data is incorrect?
If you think there is a mistake in the pre-filled spreadsheet (e.g. the wrong number of studies), please contact gwas-subs@ebi.ac.uk.