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Change z 2 beta

Merged Hanna JULIENNE requested to merge change_Z_2_beta into master
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@@ -108,11 +108,11 @@ Input
* a1: effect allele
* a2: Other allele
* 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
* pval: name of the column storing the pvalue in the gwas file. This column will be used to derive the Z-score of genetic effect.
* 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
* beta_or_z: name of the column storing the genetic effect (beta) in the gwas file. This column will be used only to retrieve the sign of the genetic effect with respect to the reference and effect allele.
* 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
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