Documentation

Phenotype Prediction

Phenotype Prediction

Using SNP effect estimation from GWAS or MLM analysis, DISSECT could be used for predicting phenotypes based on genotype data. The prediction is based on the contribution of each SNP based on their effect size and each individual genotype.

Examples

Predict phenotypes from SNP effects stored in effects.snps for individuals with genotypes specified in genotypes file.

dissect --predict --bfile genotypes --snp-effects effects.snps  --out results

Options

 

Analysis Options

--predict Predict phenotypes

 

Input Options

--bfile f Specify a genotypes file.
--bfile-list f Specify a file with a list of genotypes files.
--snp-effects f Specify the file with SNPs effects. This file must have a structure similar to the SNPs effect output of GWAS or MLM analyses. More information in MLM and GWAS.

 

Output Options

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

Output description

One file is generated after a phenotypes prediction

 Phenotypes file

file extension: .predicted.phenos

This file contains the simulated phenotypes. File without header. Their columns are:

Column 1 Family ID
Column 2 Individual ID
Cloumn 3
Predicted phenotypes
Cloumn 4
For internal use
Cloumn 5
For internal use