# Pairwise endpoint genetic correlation format

This pipeline produces a single file, containing all pairwise genetic correlations between multiple phenotypes.

Its name is structured as `finngen_R[?]_[EUR/FIN].ldsc.summary.tsv` where EUR/FIN changes based on the LD panel used.

(This refers to genetic correlation, in [Risteys](https://docs.finngen.fi/working-outside-the-sandbox/risteys-as-an-option-for-browsing-endpoints) you can also see the number of shared cases between endpoints.)

| **Column name** | **Description**                    |
| --------------- | ---------------------------------- |
| p1              | Phenotype 1                        |
| p2              | Phenotype 2                        |
| rg              | Genetic correlation                |
| se              | Standard error                     |
| z               | z-score                            |
| p               | pvalue                             |
| h2\_obs         | heritabilty of p1                  |
| h2\_obs\_se     | SE of heritability of p1           |
| h2\_int         | heritability intercept for p1      |
| h2\_int\_se     | SE of intercept                    |
| gcov\_int       | intercept of genetic covariance    |
| gcov\_int\_se   | SE of gcov                         |
| CONVERGED       | A flag if the LDSC model converged |