inbreeding coefficient (F) with vcftools

Question

[Sam]

Dear Biostars

I used the vcftools with command below to calculate inbreeding coefficient (F) of a subpopulation but the number of site (N_SITES) in the output file is much less than the sites which are available in the vcf file. The number of sites in the vcf file is about 47000 but in the output file of vcftools is 15000 and less

vcftools --vcf test.vcf --het --out test_het

output file

INDV    O(HOM)  E(HOM)  N_SITES F
401 3418    9376.7  15488   -0.97504
401.2   3397    9560.7  15850   -0.98005
A.02    7090    7906.6  12952   -0.16186
A.18    4969    9473.1  15652   -0.72896
A.25    5602    9312.6  15403   -0.60926
A.27    7218    9373.3  15524   -0.3504

would you have any idea?

Thanks

[jean.elbers]

How complete percentage-wise are the called genotypes in your VCF file? What I mean is perhaps VCFtools can only calculate F if all samples have a genotype called for a given SNP/INDEL (aka, no missing genotypes).