permuteGPAT++.md

% PERMUTEGPAT++(1) permuteGPAT++ (vcflib) | permuteGPAT++ (VCF phenotype) % Erik Garrison and vcflib contributors

NAME

permuteGPAT++

SYNOPSIS

permuteGPAT++ -f gpat.txt -n 5 -s 1

DESCRIPTION

permuteGPAT++ is a method for adding empirical p-values to a GPAT++ score.

OPTIONS

     Currently **permuteGPAT++** only supports wcFst, but will be extended.    

OUTPUT: **permuteGPAT++** will append three additional columns:
        1. The number of successes                         
        2. The number of trials                            
        3. The empirical p-value                           

file:    f   -- argument: the input file     
number:  n   -- argument: the number of permutations to run for each value [1000]
success: s   -- argument: stop permutations after 's' successes [1]

Type: phenotype

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

permuteGPAT++.cpp

LICENSE

Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.