This repository contains a software implementation of Vector Approximate Message Passing algorithm suitable for doing inference in Genome-Wide Association Studies (GWAS).
An example of a slurm script that can be used to compile and run the software:
module purge
module load gcc openmpi boost
module list
loc={a path to cpp_vamp folder}
mpic++ /$loc/main_real.cpp /$loc/vamp.cpp /$loc/utilities.cpp /$loc/data.cpp /$loc/options.cpp -march=native -DMANVECT -Ofast -g -fopenmp -lstdc++fs -D_GLIBCXX_DEBUG -o /$loc/main_real.exe
mpirun -np {number of MPI workers} /$loc/main_real.exe [input options]
Currently supported input options to C++ version of the code:
| Input option | Description |
|---|---|
run-mode |
'infere' / 'test' / 'both' |
bim-file |
filepath to .bim file including the .bim extension |
bed-file |
filepath to .bed file including the .bed extension |
bed-file-test |
filepath to .bed file reserved for testing purposes |
phen-files |
path to file containing phenotype of interest (only 1 phenotype supportet at the moment) |
phen-files-test |
path to phenotype file reserved for testing purposes |
cov-file |
filepath to .cov file including the .cov extension (covariates in a probit model) |
N |
number of individuals included in the inference process |
N-test |
number of individuals included in a testing dataset |
Mt-test |
total number of markers included in a testing dataset |
Mt |
total number of markers included in the infrence process |
out-dir |
output directory for the signal estimates |
out-name |
name of the output file |
iterations |
maximal number of iterations to be performed |
num-mix-comp |
number of gaussian mixture components used (including delta spike at zero) |
CG-max-iter |
maximal number of iteration used in conjugate gradient method for solving linear systems |
probs |
initial prior mixture coefficients (separated by comma, must sum up to 1) |
vars |
initial prior variances (separated by comma) |
rho |
initial value of damping factor |
EM-err-thr |
relative error threshold within expectation maximization |
EM-max-iter |
maximal number of iterations of expectation maximization procedure |
stop-criteria-thr |
relative error threshold within expectation maximization |
model |
regression model that describes a relationship between effect sizes and phenotypes ('linear' or 'bin_class') |
store-pvals |
indicates wheather or not the algorithm stores p-values from association tests of each of the markers |
test-iter-range |
indicates the iteration range for which R2 on a test set is calculated |
use_XXT_denoiser |
indicates whether or not a denoiser should be calculated based on formula with inversion of NxN matrix or not |
use_lmmse_damp |
indicates whether or not damping should be used in LMMSE step calculation |
h2 |
heritability value used in simulations |
CV |
number of causal variants used in simulations |
true_signal_file |
path to file containing true value of the signal |
alpha |
scaling factor applied in the normalization of a genotype matrix |
learn-vars |
indicates wheather or not prior variances are learnt |
C |
indicates the number of covariates in a probit model |
alpha-scale |
columns of genotype matrix are scaled with std^(-alpha-scale) |
gam1-init |
initial value of gam1 in the restart scenario |
gamw-init |
initial value of gamw in the restart scenario |
init-est |
indicates whether or not we initialze gVAMP with an estimate provided in estimate-file |
use-freeze |
indicates whether or not to freeze certain position in the inference process |
freeze-index-file |
a file containing 0/1 assigned to the indices that are being freezed in the inference process |
seed |
defines a seed for the gVAMP run (must be a non-negative integer) |