From 7367427b3ef3612f56a0ae4f18c6040d4c5ff275 Mon Sep 17 00:00:00 2001
From: hjulienn <hanna.julienne@pasteur.fr>
Date: Mon, 20 Feb 2023 13:34:50 +0100
Subject: [PATCH] improve documentation

---
 doc/source/index.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/index.rst b/doc/source/index.rst
index 297fd70..cabc46b 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -110,7 +110,10 @@ Input
 * freq: name of the column storing the minor allele frequence in the gwas file
 * pval: name of the column storing the pvalue in the gwas file
 * n: name of the column storing the sample size by variants (optional, will be inferred from the MAF, genetic effect and standard deviation if absent)
+* ncas: For binary traits, name of the column storing the number of cases by variants (optional)
+* ncont: For binary traits, name of the column storing the number of controls by variants (optional)
 * z: name of the column storing the genetic effect (beta) in the gwas file
+* OR : For binary traits, Odd ratio when available. Not to be confounded with the genetic effect size or 'beta'.
 * index-type: precise the type of index 
 * imputation_quality: (Optional) column containing individual-based imputation quality. Will be used to filter low quality imputation data from GWASs if the option --imputation-quality-treshold is used
 
-- 
GitLab