Diagnostic Plots for SNP quality assesment

Question

[pixie@bioinfo]

Hello, I have recently starting handling GBS data (around 115 samples). I have the filtered VCF files from two different runs. I wish to plot some SNP quality stats to compare the runs. I was specifically looking into this link: SNP quality assesment

I am interested in

1. SNP depth or Genotype depth
2. SNP observed heterozygosity
3. Depth distributions per sample for all genotype calls and for the non-missing genotype calls
4. Sample observed heterozygosity

Is there any R package which I could try ? Any other quality stats ? Thanks