This is a PLINK file, with columns separated by tabulations and no header line. It contains one line per variant with the following six fields: chromosome, variant identifier, position in morgans or centimorgans, base-pair coordinate, allele 1 and allele 2.
This is a PLINK file, with columns separated by spaces and a header line. It contains one line per sample with V+6 fields, where V is the number of variants.
To recode bed/bim/fam to raw file, use this command on PLINK:
```bash
plink --bfile$inputFile--recodeA--out$outputFile
```
Example:
FID | IID | PAT | MAT | SEX | PHENOTYPE | SNP1 | SNP2 | SNP3 | ..........
This is a text file, with columns separated by tabulations and a header line. In contains one line per individual. First column must be the individual ID.
Example:
ID | Sex | Age | LDL-C | HDL-C | HDL-D | HDL-TG | ..........
This is a csv file with columns separated by commas and a header line. This file aims at describing the role of each variable contained in the phenotypes file. For each selected variable, the user must provide a label and a binary indicator for classification as confounding factors (i.e. variables systematically included as covariates), outcome (i.e. each single variable that will be treated as a primary outcome) and candidate covariates (i.e. variables that will be assessed by CMS for inclusion as a covariate).
`Note that variables classified as confounding factor cannot be used as either outome or covariate, and such combination will be flagged as an error.`
By default, all variables in "Covariates" column will be included as covariates in each outcome analysis. The "Excluded" column give the opportunity to exclude specific variables from covariates for a given outcome. These variables must be separated by ";" without any spaces. If no variables need to be excluded, simply let the column empty. In the example, we exclude all "HDL" variable when analysing one of them.
