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

       Lennart C. Karssen

ProbABEL 0.5.0                                     4 May 2016                                        ProbABEL(1)

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

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).

       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

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

RequiredcommandlineoptionsCHROM-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!).

   Otheroptions
       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.

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

palinear(1), palogist(1), pacoxph(1)

probabelCHROM-STARTCHROM-STOPMETHODCOHORTMODELPHENOTYPE[OTHER_OPTIONS]