Changes

* <span style="color:#ff0000">The representation of Indels in a VCF file requires that no alleles in the REF and ALT field are represented with an empty string (empty allele). The red indel is an illegal VCF representation</span>

* <span style="color:#ff0000">The representation of Indels in a VCF file requires that no alleles in the REF and ALT field are represented with an empty string (empty allele). The red indel is an illegal VCF representation</span>

* <span style="color:#008000"> An indel is left aligned when the variant can no longer be shifted to the left while ensuring that no empty allele is present.  The green Indel is not left aligned.</span>

* <span style="color:#008000"> An indel is left aligned when the variant can no longer be shifted to the left while ensuring that no empty allele is present and that there is left parsimony. (meaning you cannot just add nucleotides to the left side of a variant and call it left alignment) The green Indel is not left aligned.</span>

* <span style="color:#F9A908"> The orange indel is left aligned but is not right trimmed.</span>

* <span style="color:#F9A908"> The orange indel is left aligned but is not right trimmed.</span>

* <span style="color:#0000FF"> The blue Indel is not left trimmed.</span>

* <span style="color:#0000FF"> The blue Indel is not left trimmed.</span>