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