I have done variant calling by bcftools and got vcf files for 18 different samples. Now I want to get the number of SNPs between the samples. Ref or ALT allele should be in the homozygous condition. if one samples has homozygous Ref allele and other sample has homozygous allele then take them into consideration but if both the samples has homozygous ALT allele then ignore that becouse this would not be SNP between the samples. I want to ignore the hetero condition of alleles.
I tried vcf-compare that does not seems answering what i need.