I calculated fst values by using following command, "vcftools --vcf a.vcf --weir-fst-pop pop1.txt --weir-fst-pop pop2.txt --out ex" and got negative and -nan Fst values. if i want to plot manhattan by using qqman, it appears like the below figure. I have 3 chromosome values but it's giving me one line? I used below R commands library(qqman) fst<-read.table("ex.weir.fst", header=TRUE) fstsubset<-fst[complete.cases(fst),] SNP<-c(1:(nrow(fstsubset))) mydf<-data.frame(SNP,fstsubset) manhattan(mydf,chr="CHROM",bp="POS",p="WEIR_AND_COCKERHAM_FST",snp="SNP",logp=FALSE,ylab="Weir and Cockerham Fst")

please anyone help me out to solve the problem.

Thanks

Anitha