# Sex-specific GWAS results format

There are two sets of results files for the sex-specific analyses. The first are the sex-specific results, output by REGENIE. These files are TSV [tabix-indexed](http://www.htslib.org/doc/tabix.html), compressed with bgzip and share the [GWAS results format](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/gwas-results-format).

The second set of files are those produced by meta-analysing the female- and male-specific results, conveniently combining both sexes into a single file along with a heterogeneity statistic. The format of these meta-analysis files is described in the table below.

The sex-difference results are available in the [FinnGen sex-difference PheWeb](https://sex-diff.finngen.fi/) (currently requires an active finngen.fi account). The sex-difference beta reported on PheWeb is calculated as female\_beta minus male\_beta, the sex-difference standard error (SE) is sqrt(female\_se^2 + male\_se^2) and the sex-difference P-value is the Cochran's Q P-value (all\_inv\_var\_het\_p in meta-analysis results files).

| Column name                 | Description                                                                                                                                            |
| --------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
| #CHR                        | Chromosome                                                                                                                                             |
| POS                         | Chromosomal position (GRCh38)                                                                                                                          |
| REF                         | Reference (non-effect) allele                                                                                                                          |
| ALT                         | Alternative (effect) allele                                                                                                                            |
| SNP                         | Unique CHR:POS:REF:ALT variant ID                                                                                                                      |
| female\_beta                | female-only per-allele effect of the ALT allele on endpoint (units are SDs if endpoint is continuous or logOR if endpoint is binary)                   |
| female\_se                  | standard error of the female-only effect of the ALT allele                                                                                             |
| female\_pval                | p-value of the female-only effect                                                                                                                      |
| female\_af\_alt             | allele frequency of the ALT allele in all females                                                                                                      |
| female\_af\_alt\_cases      | allele frequency of the ALT allele in female cases only                                                                                                |
| female\_af\_alt\_controls   | allele frequency of the ALT allele in female controls only                                                                                             |
| male\_beta                  | male-only per-allele effect of the ALT allele on endpoint (units are SDs if endpoint is continuous or logOR if endpoint is binary)                     |
| male\_se                    | standard error of the male-only effect of the ALT allele                                                                                               |
| male\_pval                  | p-value of the male-only effect                                                                                                                        |
| male\_af\_alt               | allele frequency of the ALT allele in all males                                                                                                        |
| male\_af\_alt\_cases        | allele frequency of the ALT allele in male cases only                                                                                                  |
| male\_af\_alt\_controls     | allele frequency of the ALT allele in male controls only                                                                                               |
| all\_meta\_N                | number of sexes contributing to meta-analysis statistics. Values of 1 indicate that the variant does not have statistics in one sex                    |
| all\_inv\_var\_meta\_beta   | meta-analysed female-male per-allele effect of the ALT allele on the endpoint - units are SDs if endpoint is continuous or logOR if endpoint is binary |
| all\_inv\_var\_meta\_sebeta | standard error of the meta-analysed female-male per-allele effect of ALT                                                                               |
| all\_inv\_var\_meta\_p      | p-value of the meta-analysed female-male per-allele effect                                                                                             |
| all\_inv\_var\_meta\_mlogp  | -log10(p-value) of the meta-analysed female-male per-allele effect                                                                                     |
| all\_inv\_var\_het\_p       | Cochran's Q heterogeneity p-value denoting significance of the difference of effect between females and males                                          |
| rsid                        | rsID of variant (if applicable)                                                                                                                        |