[Vcftools-help] Doubt about zero-coverage sites to estimate Nucleotide diversity

[Rui M M. De F. <r.m...@sh...>]

Dear all,

I have Illumina reads generated through a targeted-capture sequencing approach. 
After mapping against the reference, the bam file will contain reference regions/sites that have zero coverage because they were not targeted for sequencing,  and covered regions (with monomorphic and polymorphic sites).
In order to call a SNP, I defined that a minimum 20x coverage per sample for that site was needed. However, it is not clear to me how does vcftools counts the number of monomorphic sites. Are these all the non variable sites that are covered by at least one read after mapping? Is it the size of the reference minus the number of polymorphic sites? 

Best,

Rui