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% 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](./vcflib.md)(1)
# OTHER
## Source code
[permuteGPAT++.cpp](https://github.com/vcflib/vcflib/blob/master/src/permuteGPAT++.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
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