.TH ProbABEL 1 "4 May 2016" "ProbABEL 0.5.0"
.SH NAME
probabel \- Wrapper around the three ProbABEL binaries, simplifying their use
.SH SYNOPSIS
.B probabel
.BI "" "CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE [OTHER_OPTIONS]"
.SH DESCRIPTION
.B probabel
is a wrapper around the three ProbABEL binaries: \fBpalinear\fR,
\fBpalogist\fR, and \fBpacoxph\fR.
.PP
It is designed to simplify runnig of a Genome-Wide Association Study
(GWAS) by saving the user's precious time in two ways:
.PP
1) it runs the regression analysis of all chromosomes from \fICHROM-START\fR to
\fICHROM-STOP\fR.
.PP
2) In contrast to the three binaries mentioned above,
with \fBprobabel\fR the user doesn't need to specify the locations
of the required genetic data files. Their location is centrally
managed in a configuration file (\fI/etc/probabel_config.cfg\fR by default).

.SH OPTIONS
.SS Required command line options
.TP
.I CHROM-START
Number of the chromosome to start the analysis at.
.TP
.I CHROM-END
Number of the chromosome to end the analysis at.
.PP
Note that analysis of a single chromosome can be run by specifying the
same number for \fICHROM-START\fR and \fICHROM-STOP\fR. In fact, this
is the way to run analysis for the X or Y chromosome
.TP
.I METHOD
Which regression method to use, can be one of \fIlinear\fR,
\fIlogistic,\fR or \fIcoxph\fR.

.TP
.I COHORT
The name of the cohort as defined in the
\fI/etc/probabel_config.cfg\fR 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).
.TP
.I MODEL
The genetic model to be used. Can be either \fB--additive\fR for the
additive model (requires genotype data in dosage form), or
\fB--allmodels\fR to run all genetic models: additive, recessive,
dominant, over-dominant and 2df.
.TP
.I PHENOTYPE
The name of the phenotype file, without its extension (which should be
\fI.PHE\fR!).

.SS Other options
Any options listed after the (mandatory) previous ones will be passed
on to the underlying binary: \fBpalinear\fR, \fBpalogist\fR or
\fBpacoxph\fR, depending on the \fIMETHOD\fR.
.PP
The most commonly used option is the \fB\-o\fR option, followed by a
file name, this specifies the beginning of the file name for the
output files.

.SS Additional options
.B "\-h, \-\-help"
Get additional help on how to run \fBprobabel\fR. In this case none of
the other options needs to be specified.

.SH EXAMPLES
This runs a genome-wide association scan using linear regression and
the additive genetic model on cohort \fIMy_Large_Cohort\fR for
phenotype \fImy_phenotype\fR:
.PP
.nf
.RS
probabel 1 22 linear "My_Large_Cohort" \-\-additive my_phenotype
.RE
.fi
.PP

.SH "SEE ALSO"
palinear(1), palogist(1), pacoxph(1)
.SH BUGS
The bugtracker is located at
.br
https://github.com/GenABEL-Project/ProbABEL/issues
.SH AUTHORS
Lennart C. Karssen