Plink and VCFTools can be used create missingness per sample (.imiss) and per variants (.lmiss) files from VCF files.

https://www.cog-genomics.org/plink2/basic_stats#missing

http://vcftools.sourceforge.net/man_latest.html (--missing-indv, --missing-site)

Example first lmiss file records:

CHR      SNP        N_MISS   N_GENO   F_MISS
chr_1    id_1       10       100      0.10
chr_1    id_2       20       100      0.20
chr_1    id_2       30       100      0.30
potentially millions more variants

Example first imiss file recods

   FID       IID       MISS_PHENO   N_MISS   N_GENO   F_MISS
  Sample_1   Sample_1  Y            5000     100000   0.05
  Sample_2   Sample_2  Y            10000    100000   0.10
  Sample_3   Sample_3  Y            15000    100000   0.15
  Sample_4   Sample_4  Y            20000    100000   0.20
  Sample_5   Sample_5  Y            50000    100000   0.50
  potentially thousands more samples

I am probably not the first (or last) person who would like to plot this data to get an idea of the generall missingniss of his data.

Anyone a good existing (python) script for this?