I'm getting some really confusing results using vcftools and I was wondering if anyone could shed some light. I have merged 5 individual SNP call .vcf files using vcf-merge. This merged file seems fine until I try to calculate allele frequency from it (--freq). Some of the allele freq are correct (compared to calculating by hand) but some are wrong. The Fst calculator (--fst-pop) also throws up some weird highly negative scores.
The genotype scores for the individuals all seem to be correct (the same as the source files) in the rows that give wrong allele frequencies, so how is vcftools getting an incorrect value?
Any help would be greatly appreciated,