Documentation

Genome-Wide Association Studies

Description

DISSECT can conduct individual association tests on each SNP as in genome-wide association analysis, or testing for association arbitrary groups of SNPs. Associations was computed adjusting a linear model.

Examples

Perform a GWAS analysis testing each SNP in genotype file individually:

dissect --gwas –bfile genotypes –pheno individuals.phenos  --out results

Perform GWAS analysis fitting all SNPs in each genotype file at same time. Different genotype files are specified in genotypes.list.

dissect --gwas --bfile-list genotypes.list --group-all --pheno individuals.phenos --out results

Perform GWAS correcting by a GRM using a LMM model (new in version 1.15.2c):

dissect --gwas --bfile-grm-list genotypes-grm.list --pheno individuals.phenos --covar covars.dat --qcovars qcovars.dat --out results

Options

 

Analysis Options

--gwas  Perform genome-wide association analysis

Input Options

--bfile f Specify a genotypes file.
--bfile-list f Specify a file with a list of genotypes files.
--bfile-grm-list f (new in version 1.15.2c) Specify a file with a list of genotype, grm file pairs. The first column has to contain the genotype file, the second column, the GRM used for correcting the corresponding genotype file. Provided GRMs should be diagonalized GRMs (i.e. computed with the --diagonalize option).
--pheno f Specify the phenotypes file.
--covar f Specify the discrete covariates file 1.
--qcovar f Specify the quantitative covariates file 1.

Output Options

--out f Specify the base name for output files.

 

Other

--pheno-col n Specify which column use from phenotypes file. (default n = 1)
--groups f Fit SNPs in same group together. The groups will be those specified in the groups file, f.

Output description

Different output files could be generated from GWAS analysis depending on the specified options. If genotype files are passed using –bfile-list option, there will be a an set of output files for each genotype file.

Mean and Covariates files

file extensions: .gwas.mean, .gwas.discrete, .gwas.quantitative

This file contains estimated effects for each covariate in the model. Columns are:

GROUP Group of SNPs used for fitting the model. SNP name if tested individually.
NAME Name of the covariate
BETA Covariate effect
SE Standard error
PV Estimated p-value. It only can  be estimated if DISSECT is compiled with BOOST libraries. -1 otherwise.

SNP effects

file extensions: .gwas.snps

This file contains estimated effects for each covariate in the model. Columns are:

GROUP Group of SNPs used for fitting the model. SNP name if tested individually.
SNP SNP name
ALLELE Reference allele
MEAN SNP mean (i.e. \(2p\), where p is the reference allele frequency)
STDEV SNP standard deviation (i.e. \(\sqrt{2p(1-p)}\), where p is the reference allele frequency)
BETA SNP effect
NBETA Normalized SNP effect by SNP standard deviation (i.e. BETA/STDEV)
SE Standard error
PV Estimated p-value. It only can be estimated if DISSECT is compiled with BOOST libraries. -1 otherwise.
GROUPPV Estimated group p-value. It only can be estimated if DISSECT is compiled with BOOST libraries. -1 otherwise.