I am trying to use bcftools isec to find common variants between two callers. it mostly works find but when it is a tandem mutation e.g.CC>TT or GG>AA.. mutations instead of an SNP. It is not included in the intersect file? I have two vcf files that have five common tandem mutations. All five of these mutations were excluded from the interest files (0002 or 0003.txt) and all the single point mutations were correct. why is that? is there any way to include the tandem mutations as well?
bcftools isec A.vcf B.vcf -p common_mutations/