Config.txt

#All lines that starts with "#" are considered comments, so it will be ignored

#Inputs
Input	X	Typed	/home/path/target/genotypedX.vcf.gz
Input	Autosomal	Typed	/home/path/target/genotypedAuto.vcf.gz
Input	X	Imputed	/home/path/target/imputedX.vcf.gz

#For covar we request the covar file and the phenotype column name
Input	covar	COVAR.txt	disease

#Reference
Reference	X	/home/path/ref/refX.vcf.gz
#Reference	Autosomal	/home/path/ref/refAuto.vcf.gz

#PCA Outliers
Outlier	X	No
Outlier	X	Yes
Outlier	Autosomal	No
Outlier Autosomal	Yes

#Number of PCs
Outlier PC  X   5
Outlier PC  Autosomal   6

#PCA regression
#PCA	X
#PCA	Autosomal

#Regression model
#Model	Script	./XWAS_v2/Analysis/selectModel.R
Model	Regression  DISEASE~AGE+SEX+PC1+PC2+PC3+PC4+PC5+PC6+PC7+PC8+PC9+PC10

#Programs
Programs	Plink1	plink
Programs	Plink2	plink2
Programs	GCTA	/home/path/programs/gcta64
Programs	GWAMA	/home/path/programs/GWAMA
Programs	R	Rscript