Comparing two VCF files from command line

For convenience a common operation of VCF comparison can be done from command line like this:

$ python3 -m genomvar compare_vcf vcf1.vcf vcf2.vcf > comparison.vcf
Unit variants:
   first only: 1
   second only: 2
   both: 105

The numbers can be used for plotting Venn diagram and indicate corresponding patch sizes.

File comparison.vcf will contain something like this:

chr1    18353435        .       C       G       100     .       mt=SNP;whichVCF=both;ln=186;ln2=374
chr1    18704102        .       T       A       100     .       mt=SNP;whichVCF=both;ln=187;ln2=375

INFO fields indicate which VCF contains the variant on the line. ln and ln2 indicate line numbers in original files.