vcftools - Fst statistics

Question

[Lukas]

I have .vcf file with over 78000 variations in 95 experiment subjects. I used vcftools to extract fixation index score for general differentiation between Case and Control groups.

./vcftools --vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf --weir-fst-pop Case.txt --weir-fst-pop Control.txt --out FstExon_Case_vs_Control

After filtering, kept 95 out of 95 Individuals
Outputting Weir and Cockerham Fst estimates.
        Fst: Only using diploid sites.
Weir and Cockerham mean Fst estimate: -0.00031927
Weir and Cockerham weighted Fst estimate: -0.00047509
After filtering, kept 78758 out of a possible 78758 Sites

But when I tried to open .weir.fst files with notepad or excel, I lost over 9 000 rows of data. I am sure that there is problem with how I am opening the .weir.fst files.

Please, how are these files opened properly?