---
name: "probabel.pl"
section: "1"
platform: "linux"
package: "probabel"
version: "0.5.0+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/probabel.pl"
---

# probabel.pl(1)

Wrapper around the three ProbABEL binaries, simplifying their use

## NAME

probabel - Wrapper around the three ProbABEL binaries, simplifying their use

## SYNOPSIS

**probabel***CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE \[OTHER\_OPTIONS\]*

## DESCRIPTION

**probabel** is a wrapper around the three ProbABEL binaries: **palinear**, **palogist**, and **pacoxph**.

It is designed to simplify runnig of a Genome-Wide Association Study (GWAS) by saving the user's precious time in two ways:

1\) it runs the regression analysis of all chromosomes from *CHROM-START* to *CHROM-STOP*.

2\) In contrast to the three binaries mentioned above, with **probabel** the user doesn't need to specify the locations of the required genetic data files. Their location is centrally managed in a configuration file (*/etc/probabel\_config.cfg* by default).

## OPTIONS

### Required command line options

- *CHROM-START*

  Number of the chromosome to start the analysis at.

- *CHROM-END*

  Number of the chromosome to end the analysis at.

Note that analysis of a single chromosome can be run by specifying the same number for *CHROM-START* and *CHROM-STOP*. In fact, this is the way to run analysis for the X or Y chromosome

- *METHOD*

  Which regression method to use, can be one of *linear*, *logistic,* or *coxph*.

- *COHORT*

  The name of the cohort as defined in the */etc/probabel\_config.cfg* file. Using the cohort identifier from the config file the three actual ProbABEL binaries know where to find the genotypic information files (dosage files and/or probability files).

- *MODEL*

  The genetic model to be used. Can be either **--additive** for the additive model (requires genotype data in dosage form), or **--allmodels** to run all genetic models: additive, recessive, dominant, over-dominant and 2df.

- *PHENOTYPE*

  The name of the phenotype file, without its extension (which should be *.PHE*!).

### Other options

Any options listed after the (mandatory) previous ones will be passed on to the underlying binary: **palinear**, **palogist** or **pacoxph**, depending on the *METHOD*.

The most commonly used option is the **-o** option, followed by a file name, this specifies the beginning of the file name for the output files.

### Additional options

**-h, --help** Get additional help on how to run **probabel**. In this case none of the other options needs to be specified.

## EXAMPLES

This runs a genome-wide association scan using linear regression and the additive genetic model on cohort *My\_Large\_Cohort* for phenotype *my\_phenotype*:

```
probabel 1 22 linear "My_Large_Cohort" --additive my_phenotype
```

## SEE ALSO

[palinear(1)](/palinear/1.md), [palogist(1)](/palogist/1.md), [pacoxph(1)](/pacoxph/1.md)

## BUGS

The bugtracker is located at\
 https://github.com/GenABEL-Project/ProbABEL/issues

## AUTHORS

Lennart C. Karssen