I have a merged .vcf file, that although wasn't merged using vcftools seems almost identical to vcf-merge files. If I try and use --freq to calculate allele frequencies from this file I get the error message "Require Genotypes in VCF file in order to output Frequency Statistics". This seems odd as the file has the same GT:GQ:PL format as other .vcf files.
I was wondering if anyone knows what vcftools uses to calculate --freq and why I am getting this error message. I have gone back to source files, merged these in vcftools then performed --freq with this file, this time the analysis "works" but I get incorrect allele frequencies (compared to working them out by hand).