system("sed 's/,\t/,/g' phase1_integrated_calls.20101123.ALL.panel > phase1_integrated_calls.20101123.ALL.panel.4col")

indit <- read.table("phase1_integrated_calls.20101123.ALL.panel.4col", header = FALSE, sep = "\t", quote = "",as.is=TRUE)

indi1 <- as.vector(unlist(rbind(indit[,1],indit[,1])))
indi2 <- as.vector(unlist(rbind(indit[,2],indit[,2])))
indi3 <- as.vector(unlist(rbind(indit[,3],indit[,3])))
indi4 <- as.vector(unlist(rbind(indit[,4],indit[,4])))

indi4 <- gsub(",",";",indi4)

indi <- cbind(indi1,indi2,indi3,indi4)

save(indi,file="individuals.Rda")


# EUeuropeans <- c(which(indi[,2]=="CEU"),which(indi[,2]=="FIN"),which(indi[,2]=="GBR"),which(indi[,2]=="IBS"),which(indi[,2]=="TSI"))

EUeuropeans <- c(which(indi[,3]=="EUR"))

                 
EUeurop <- as.integer(sort.int(as.integer(unique(EUeuropeans))))

indi_EUeurop <- indi[EUeurop,]

save(indi_EUeurop,file="individualsEU.Rda")



annot <- read.table("ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes_annot.txt",header = FALSE, sep = " ", quote = "",as.is = TRUE,skip=2)



for (i in 3:9) {

    annot[[i]] <- gsub(",",";",annot[[i]])

}

save(annot,file="annotation_chr1.Rda")



sPF <- samplesPerFeature(X="ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes_mat",samples=EUeurop,lowerB=1.5,upperB=0.05*length(EUeurop))

save(sPF,file="sPF_15_005_chr1_EU.Rda")


lii <- length(indi[,1])
samples <- 1:lii

sPF <- samplesPerFeature(X="ALL.chr1.phase1_release_v3.20101123.snps_indels_svs.genotypes_mat",samples=samples,lowerB=1.5,upperB=0.05*lii)

save(sPF,file="sPF_15_005_chr1.Rda")