The VCF spec includes the option of having a CIGAR string for each alternate variant to describe how it aligns/differs from the reference allele. This would be an alternative the the current SNVPOS field we are using to record SNP positions and would be more flexible for future exertions to MNP or Indel basis variants. It would also simplify identification of the set of variations actually present in the observed haplotypes rather than the set all basis SNP positions recorded by SNVPOS (many of which may not be used).
The VCF spec includes the option of having a CIGAR string for each alternate variant to describe how it aligns/differs from the reference allele. This would be an alternative the the current SNVPOS field we are using to record SNP positions and would be more flexible for future exertions to MNP or Indel basis variants. It would also simplify identification of the set of variations actually present in the observed haplotypes rather than the set all basis SNP positions recorded by SNVPOS (many of which may not be used).